From ben.cook at griffith.edu.au Thu Oct 1 16:54:33 2009 From: ben.cook at griffith.edu.au (Ben Cook) Date: Fri, 2 Oct 2009 09:54:33 +1000 Subject: [Mesquitelist] question on use of Mesquite Message-ID: Dear Mesquite users I am new to Mesquite and have a ML tree (from PHYML) and I would like to calculate Slatkin and Maddison's s for this observed tree, then compare the observed s with a simulated distribution of s given for different scenarios/hypotheses. In my file, I have: - the taxa block corresponding to the mtDNA sequences - a taxa block corresponding to the populations - an association between the two taxa blocks (plus have the sequences color coded as population 'groups') - the above mentioned gene tree is also included (although I am unsure if I have included it properly - but I can view it in a tree window) When I go to to the 'Legend' menu from the tree window, and select s, the following message appears: 'A command could not be completed because an exception occurred (i.e. a crash; class java.lang.NullPointerException ). WARNING: there is a chance this crash could have corrupted your data. Please check your data carefully. If you save any files, you might best use Save As... in case file saving doesn't work properly.' I have used both the standard Mesquite, and the 1 G version, and the same message appears. Any ideas on how to solve this problem would be greatly appreciated best regards Ben Dr. Ben Cook Australian Rivers Institute Griffith University Nathan Queensland AUSTRALIA 4111 ph +61 7 3735 7418 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091002/84fe4698/attachment.html From wmaddisn at interchange.ubc.ca Thu Oct 1 19:21:59 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 01 Oct 2009 19:21:59 -0700 Subject: [Mesquitelist] question on use of Mesquite In-Reply-To: References: Message-ID: Ben, Could you send me a copy of your file (off list) so that I could diagnose? thanks, Wayne At 9:54 AM +1000 2.10.2009, Ben Cook wrote: >Dear Mesquite users > >I am new to Mesquite and have a ML tree (from PHYML) and I would >like to calculate Slatkin and Maddison's s for this observed tree, >then compare the observed s with a simulated distribution of s given >for different scenarios/hypotheses. > >In my file, I have: >- the taxa block corresponding to the mtDNA sequences >- a taxa block corresponding to the populations >- an association between the two taxa blocks (plus have the >sequences color coded as population 'groups') >- the above mentioned gene tree is also included (although I am >unsure if I have included it properly - but I can view it in a tree >window) > >When I go to to the 'Legend' menu from the tree window, and select >s, the following message appears: >'A command could not be completed because an exception occurred >(i.e. a crash; class java.lang.NullPointerException ). WARNING: >there is a chance this crash could have corrupted your data. Please >check your data carefully. If you save any files, you might best >use Save As... in case file saving doesn't work properly.' > >I have used both the standard Mesquite, and the 1 G version, and the >same message appears. > >Any ideas on how to solve this problem would be greatly appreciated > > >best regards >Ben > > >Dr. Ben Cook >Australian Rivers Institute >Griffith University >Nathan Queensland AUSTRALIA 4111 >ph +61 7 3735 7418 > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From hanleyd at uwindsor.ca Fri Oct 2 10:58:31 2009 From: hanleyd at uwindsor.ca (Daniel Hanley) Date: Fri, 2 Oct 2009 13:58:31 -0400 Subject: [Mesquitelist] problem importing tree to R Message-ID: <000101ca4389$f6dc1740$e49445c0$@ca> Dear Mail List Members, I have been making a large phylogeny in Mesquite for quite a while that no longer appears to import into R. I believe this is an issue with the formatting in Mesquite and am looking for guidance in how to export it so that it is readable by other programs. The particular tree has close to 700 tips and some polytomies. It also has colored branches, and annotated branches in various spots within the tree). This has made the nexus code rather sloppy. I've tried everything to get this to be read into R with read.nexus function, but it dosen't appear to be. The formatting stays in the nexus file despite the format it is exported as. It is present even when I export as Phyllip. I also have tried manually removing the clutter, but that didn't work either. The reason I don't think it's an issue with R, is because it used to import this tree, and it still imports a larger unformatted tree (~9,000 tips). If anyone could give me some guidance I would greatly appreciate it. Best, Daniel _______________________________ Daniel Hanley PhD Candidate Department of Biological Sciences 401 Sunset Avenue, Biology Building University of Windsor Windsor, Ontario, Canada, N9B 3P4 Phone: (519) 253-3000 ext 2704 Fax: (519) 971-3609 http://www.uwindsor.ca/hanleyd -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091002/d1f5dbd2/attachment.html From hanleyd at uwindsor.ca Fri Oct 2 12:52:33 2009 From: hanleyd at uwindsor.ca (Daniel Hanley) Date: Fri, 2 Oct 2009 15:52:33 -0400 Subject: [Mesquitelist] problem importing tree to R In-Reply-To: <14159_1254506326_n92HwiGk015881_000101ca4389$f6dc1740$e49445c0$@ca> References: <14159_1254506326_n92HwiGk015881_000101ca4389$f6dc1740$e49445c0$@ca> Message-ID: <002301ca4399$e6871470$b3953d50$@ca> I wanted to specify too that within the *.nex file the annotated notes and colors appear the in TREE section (that has the nexus file information), as well as after (Begin MESQUITE; . setTree) on the problem file. But whenever I normally add annotations and colors it can be read in a text editor only after Begin MESQUITE; .setTree. A mock example of a working file is below (in the problem file these would both be the same): TREE Tree_for_passeriformes = ((1,2,3),(((((4,5,6,7,8,9,10),(11,12,13,14,15,16,17,18,19,20,21),(22,23,24,2 5,26,27,28,29,30,31,32,33,34,35,36)),((((37,38),(39,40)),(41,((42,43),(((44, 45),(46,47)),(48,49))))),50,((51,52,53),(54,55,56)))),(((57,58,59,60),(((((6 1,62,63,(64,65)),((66,((67,68),69,(70,71,72,(73,74,75),76,77),(78,79,80,81,8 2,83,84,85,86,87),88,89,90,91,92,93,94,(95,96),97)),((98,99,100,101,102,103, 104,105,106),(107,(108,109),110,111))),(((112,(113,114)),((115,116,117,118), (119,120,121,122,123)),(124,125),126),(((127,128,129,130,131,132,133,134,135 ,136,137,138),(139,140)),((141,142,143,144,145,146,147,148),(149,150,151,152 ,153,154,155))),156),(157,158),(((((159,160,161,162),163),((164,(((165,166), (167,168)),(169,170))),(171,172,173))),((174,175,176),(177,178)),(179,180,18 1,182),((183,(184,185)),186,187)),(188,((189,190,191,192,193,194,195),196))) ,(197,198),199,200,201),(202,(203,204,205,206),(207,((208,(209,210)),((211,2 12),((213,214),(215,216))))),((((217,218),((((219,220),221,222),(223,224),(2 25,226,227,228,229),(230,231),232,(233,234)),(235,236))),(237,(238,239),(((2 40,241),242),243))),(((244,245,246,247,248,249,250),(251,252,253,254,255,256 ,257,258,259,260,261,262,263,264,265)),266)),((267,268,269),270,271))),(272, 273,274,275,276,277),(278,(279,280)),281),((282,283,284,285,286,287,288,289, 290),(291,292))),(((293,294,295,296,297,298,299,300,301,302,303,304,305,306, 307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323),(((324, 325,326,327,328,329,330,331),(332,333)),(334,335,336,337,338,339,340,341,342 ))),((343,(344,345,346),(347,348),349,350,351,352,(353,354),355,356,(357,358 ,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377 ,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396 ,397,398)),(((399,400,401,402,403,404,405),(406,407,408,409,410,411)),(((412 ,413,414,415,416,417),(418,419,420,421,422,423,424,425,426,427),428),((((429 ,430),(431,432)),433,((((((434,435),(436,437)),(438,439,440,441,442,443,444, 445,446,447,448,449,450)),(451,452,453,454,455,456,457,458),((459,460),461,4 62)),((463,464),((465,466,467,468,469,470,471,472,473,474),((((((475,(476,47 7,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,49 6,497,498,499,500,501,502,503,504,505,506,507,508,509)),(510,511)),(512,(513 ,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532 ,533))),((534,535,536,537),(538,539,540,541,542,543,544,545,546,547,548,549, 550,551,552,553,554,555,556,557,558,559,560))),(((561,562,563,564,565,566,56 7,568),569),570)),571,572,573,574,575,(576,577),(578,579)),(580,581,582,583) ,584,585,(586,587,588,589,590,591,592,593,594,595))),(596,(597,598,599),(600 ,601))),((602,603),604,605,(606,607,608,609),610),611,612,(613,614),(615,616 ),(((((617,618,619),(620,621,622,623)),624),((625,626,627,628,629,630,631,63 2,633,634),635)),636,((637,638,639,640,641,642,643),((644,645,646,647,648,64 9,650,651,652),(653,654))))),(655,656)),((657,(((658,659,660,661,662,663),(( 664,665),666)),(((667,668,669,670,671,672,673,674),(675,676,677,678,679,680, 681,682,683,684,685,686,687,688,689),690,(691,692,693,694,695)),((696,697),( (698,699,700,701),(702,703,704,705)),(706,707,708,709,710))))),(711,712,713, 714)))))))),(715,716,717,718,719))),((((((((((720,721,722,723,724,725,726,72 7),(728,729,730,731),732,(733,734),(735,736,737,738),(739,740),(741,742),743 ,(744,745,746,747,748,749),750,(751,752,753,754,755,756,757,758,759,760,761) ,(762,763),(764,765)),(((766,(767,768),((((((((769,((((((((770,(771,772)),(7 73,774)),((775,776),777)),(778,779)),780),781,782),(((783,784),785),(((((786 ,(787,788)),789),790),791),792))),793,(((((((((((794,795),(796,797)),798),(7 99,800)),801),(802,803)),(804,(805,806))),807),808),(((((((809,810),811),(81 2,813)),(814,815)),816),((817,818),819)),(((820,(821,822)),(823,824)),825))) ,826,827),(((((((((828,829),830),(831,832)),(833,834)),((835,836),837)),838, ((839,840),841)),((842,843),844),845),(((846,(((847,848),849),850),851,852), 853),((854,(855,856)),(857,858)),(859,860,861),((((862,863),864),865),866))) ,867),((868,869),(870,871,872,((873,874),875),876,877)))),878,(879,880)),(88 1,882)),883),884),885),886),(887,888))),((889,(890,(891,892))),((893,894),(( 895,(896,897)),(898,899,900,901)))),902),903,904,((905,(906,907)),((908,909) ,(910,(911,912),913,914,915,(916,(917,918)),(919,920,(921,922,923),924),925, 926)))),(((927,928),(929,930,931,(932,(933,934,935,936,937)))),938)),(939,94 0,941,942,943,(944,945),946,(947,948),(949,950),((((951,952),953),954),955,( 956,957),(958,959),(960,961)),(962,963,((964,965),966,(967,968),969,(970,971 ))))),972,973,974),975),976),(977,978,979,(980,981))),(982,983)),(984,985))) ); END; Begin MESQUITE; ... setTreeNumber 1; setTree '((1,2,3),(((((4,5,6,7,8,9,10),(11,12,13,14,15,16,17,18,19,20,21),(22,23,24, 25,26,27,28,29,30,31,32,33,34,35,36)),((((37,38),(39,40)),(41,((42,43),(((44 ,45),(46,47)),(48,49))))),50,((51,52,53),(54,55,56)))),(((57,58,59,60),(((((61,62,63,(64,65)),((66,((67,68),69,(70,71,72,(73,74,7 5),76,77),(78,79,80,81,82,83,84,85,86,87),88,89,90,91,92,93,94,(95,96),97)), ((98,99,100,101,102,103,104,105,106),(107,(108,109),110,111))),(((112,(113,1 14)),((115,116,117,118),(119,120,121,122,123)),(124,125),126),(((127,128,129 ,130,131,132,133,134,135,136,137,138),(139,140)),((141,142,143,144,145,146,1 47,148),(149,150,151,152,153,154,155))),156),(157,158),(((((159,160,161,162) ,163),((164,(((165,166),(167,168)),(169,170))),(171,172,173))),((174,175,176 ),(177,178)),(179,180,181,182),((183,(184,185)),186,187)),(188,((189,190,191 ,192,193,194,195),196))),(197,198),199,200,201),(202,(203,204,205,206),(207, ((208,(209,210)),((211,212),((213,214),(215,216))))),((((217,218),((((219,22 0),221,222),(223,224),(225,226,227,228,229),(230,231),232,(233,234)),(235,23 6))),(237,(238,239),(((240,241),242),243))),(((244,245,246,247,248,249,250), (251,252,253,254,255,256,257,258,259,260,261,262,263,264,265)),266)),((267,2 68,269),270,271))),(272,273,274,275,276,277),(278,(279,280)),281),((282,283, 284,285,286,287,288,289,290),(291,292))),(((293,294,295,296,297,298,299,300, 301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319, 320,321,322,323),(((324,325,326,327,328,329,330,331),(332,333)),(334,335,336 ,337,338,339,340,341,342))),((343,(344,345,346),(347,348),349,350,351,352,(3 53,354),355,356,(357,358,359,360,361,362,363,364,365,366,367,368,369,370,371 ,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390 ,391,392,393,394,395,396,397,398)),(((399,400,401,402,403,404,405),(406,407, 408,409,410,411)),(((412,413,414,415,416,417),(418,419,420,421,422,423,424,4 25,426,427),428),((((429,430),(431,432)),433,((((((434,435),(436,437)),(438, 439,440,441,442,443,444,445,446,447,448,449,450)),(451,452,453,454,455,456,4 57,458),((459,460),461,462)),((463,464),((465,466,467,468,469,470,471,472,47 3,474),((((((475,(476,477,478,479,480,481,482,483,484,485,486,487,488,489,49 0,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,50 9)),(510,511)),(512,(513,514,515,516,517,518,519,520,521,522,523,524,525,526 ,527,528,529,530,531,532,533))),((534,535,536,537),(538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,56 0))),(((561,562,563,564,565,566,567,568),569),570)),571,572,573,574,575,(576,577),(578,579)),(580,581,582,583),584,585,(586,5 87,588,589,590,591,592,593,594,595))),(596,(597,598,599),(600,601))),((602,6 03),604,605,(606,607,608,609),610),611,612,(613,614),(615,616),(((((617,618, 619),(620,621,622,623)),624),((625,626,627,628,629,630,631,632,633,634),635) ),636,((637,638,639,640,641,642,643),((644,645,646,647,648,649,650,651,652), (653,654))))),(655,656)),((657,(((658,659,660,661,662,663),((664,665),666)), (((667,668,669,670,671,672,673,674),(675,676,677,678,679,680,681,682,683,684 ,685,686,687,688,689),690,(691,692,693,694,695)),((696,697),((698,699,700,70 1),(702,703,704,705)),(706,707,708,709,710))))),(711,712,713,714)))))))),(71 5,716,717,718,719))),((((((((((720,721,722,723,724,725,726,727),(728,729,730 ,731),732,(733,734),(735,736,737,738),(739,740),(741,742),743,(744,745,746,7 47,748,749),750,(751,752,753,754,755,756,757,758,759,760,761),(762,763),(764 ,765)),(((766,(767,768),((((((((769,((((((((770,(771,772)),(773,774)),((775, 776),777)),(778,779)),780),781,782),(((783,784),785),(((((786,(787,788)),789 ),790),791),792))),793,(((((((((((794,795),(796,797)),798),(799,800)),801),( 802,803)),(804,(805,806))),807),808),(((((((809,810),811),(812,813)),(814,815) ),816),((817,818),819)),(((820,(821,822)),(823,824)),825))),826,827),((((((( ((828,829),830),(831,832)),(833,834)),((835,836),837)),838,((839,840),841)),((842,843),844),845),(( (846,(((847,848),849),850),851,852),853),((854,(855,856)),(857,858)),(859,860,861),((((862,863),864),865),866))),8 67),((868,869),(870,871,872,((873,874),875),876,877)))),878,(879,880)),(881, 882)),883),884),885),886),(887,888))),((889,(890,(891,892))),((893,894),((89 5,(896,897)),(898,899,900,901)))),902),903,904,((905,(906,907)),((908,909),( 910,(911,912),913,914,915,(916,(917,918)),(919,920,(921,922,923),924),925,92 6)))),(((927,928),(929,930,931,(932,(933,934,935,936,937)))),938)),(939,940, 941,942,943,(944,945),946,(947,948),(949,950),((((951,952),953),954),955,(95 6,957),(958,959),(960,961)),(962,963,((964,965),966,(967,968),969,(970,971)) ))),972,973,974),975),976),(977,978,979,(980,981))),(982,983)),(984,985)))); '; Thanks sorry for two emails. Daniel _______________________________ Daniel Hanley PhD Candidate Department of Biological Sciences 401 Sunset Avenue, Biology Building University of Windsor Windsor, Ontario, Canada, N9B 3P4 Phone: (519) 253-3000 ext 2704 Fax: (519) 971-3609 http://www.uwindsor.ca/hanleyd From: mesquitelist-bounces at mesquiteproject.org [mailto:mesquitelist-bounces at mesquiteproject.org] On Behalf Of Daniel Hanley Sent: 2-October-09 1:59 PM To: mesquitelist at mesquiteproject.org Subject: [Mesquitelist] problem importing tree to R Dear Mail List Members, I have been making a large phylogeny in Mesquite for quite a while that no longer appears to import into R. I believe this is an issue with the formatting in Mesquite and am looking for guidance in how to export it so that it is readable by other programs. The particular tree has close to 700 tips and some polytomies. It also has colored branches, and annotated branches in various spots within the tree). This has made the nexus code rather sloppy. I've tried everything to get this to be read into R with read.nexus function, but it dosen't appear to be. The formatting stays in the nexus file despite the format it is exported as. It is present even when I export as Phyllip. I also have tried manually removing the clutter, but that didn't work either. The reason I don't think it's an issue with R, is because it used to import this tree, and it still imports a larger unformatted tree (~9,000 tips). If anyone could give me some guidance I would greatly appreciate it. Best, Daniel _______________________________ Daniel Hanley PhD Candidate Department of Biological Sciences 401 Sunset Avenue, Biology Building University of Windsor Windsor, Ontario, Canada, N9B 3P4 Phone: (519) 253-3000 ext 2704 Fax: (519) 971-3609 http://www.uwindsor.ca/hanleyd -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091002/e90f6d7e/attachment-0001.html From wmaddisn at interchange.ubc.ca Sun Oct 4 13:50:36 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 04 Oct 2009 13:50:36 -0700 Subject: [Mesquitelist] problem importing tree to R In-Reply-To: <3860_1254513193_1254513193_002301ca4399$e6871470$b3953d50$@ca> References: <14159_1254506326_n92HwiGk015881_000101ca4389$f6dc1740$e49445c0$@ca> <3860_1254513193_1254513193_002301ca4399$e6871470$b3953d50$@ca> Message-ID: Mesquite uses the format only within the Mesquite block; elsewhere in the NEXUS file, such as in a TREES block, it uses the [% annotation] format. Make sure that you are saving the trees to a TREES block or external file so that the second format is used. This second format should be readable by a program compliant with the Newick tree standard, because the Newick standard defines [] as skippable comments. Perhaps you are using a function in R that is not fully compliant with the Newick standard? The alternative is to show the tree in the tree window, and go to the text view (see small tabs "Graphics", "Text", "Parameters", etc. You will see a line "Tree Description:". What is given is a cleaned version of the Newick string defining the tree; the extra annotations are not included. For future versions we will add a function to export trees without any comments in case your other program isn't able to handle them. Wayne At 3:52 PM -0400 2.10.2009, Daniel Hanley wrote: >Content-type: multipart/alternative; > boundary="Boundary_(ID_f1kEXeN4KbHgFS+SrDk2Mw)" >Content-language: en-ca > >I wanted to specify too that within the *.nex file the annotated >notes and colors appear the in TREE section (that has the nexus file >information), as well as after (Begin MESQUITE; ? setTree) on the >problem file. But whenever I normally add annotations and colors it >can be read in a text editor only after Begin MESQUITE; ?setTree. > >A mock example of a working file is below (in the problem file these >would both be the same): >TREE Tree_for_passeriformes = >((1,2,3),(((((4,5,6,7,8,9,10),(11,12,13,14,15,16,17,18,19,20,21),(22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)),((((37,38),(39,40)),(41,((42,43),(((44,45),(46,47)),(48,49))))),50,((51,52,53),(54,55,56)))),(((57,58,59,60),(((((61,62,63,(64,65)),((66,((67,68),69,(70,71,72,(73,74,75),76,77),(78,79,80,81,82,83,84,85,86,87),88,89,90,91,92,93,94,(95,96),97)),((98,99,100,101,102,103,104,105,106),(107,(108,109),110,111))),(((112,(113,114)),((115,116,117,118),(119,120,121,122,123)),(124,125),126),(((127,128,129,130,131,132,133,134,135,136,137,138),(139,140)),((141,142,143,144,145,146,147,148),(149,150,151,152,153,154,155))),156),(157,158),(((((159,160,161,162),163),((164,(((165,166),(167,168)),(169,170))),(171,172,173))),((174,175,176),(177,178)),(179,180,181,182),((183,(184,185)),186,187)),(188,((189,190,191,192,193,194,195),196))),(197,198),199,200,201),(202,(203,204,205,206),(207,((208,(209,210)),((211,212),((213,214),(215,216))))),((((217,218),((((219,220),221,222),(223,224),(22 5 >,226,227,228,229),(230,231),232,(233,234)),(235,236))),(237,(238,239),(((240,241),242),243))),(((244,245,246,247,248,249,250),(251,252,253,254,255,256,257,258,259,260,261,262,263,264,265)),266)),((267,268,269),270,271))),(272,273,274,275,276,277),(278,(279,280)),281),((282,283,284,285,286,287,288,289,290),(291,292))),(((293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323),(((324,325,326,327,328,329,330,331),(332,333)),(334,335,336,337,338,339,340,341,342))),((343,(344,345,346),(347,348),349,350,351,352,(353,354),355,356,(357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398)),(((399,400,401,402,403,404,405),(406,407,408,409,410,411)),(((412,413,414,415,416,417),(418,419,420,421,422,423,424,425,426,427),428),((((429,430),(431,432)),433,((((((434,435),(436,437)),(438,439,440,441,442,443,444,445 , >446,447,448,449,450)),(451,452,453,454,455,456,457,458),((459,460),461,462)),((463,464),((465,466,467,468,469,470,471,472,473,474),((((((475,(476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509)),(510,511)),(512,(513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533))),((534,535,536,537),(538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560))),(((561,562,563,564,565,566,567,568),569),570)),571,572,573,574,575,(576,577),(578,579)),(580,581,582,583),584,585,(586,587,588,589,590,591,592,593,594,595))),(596,(597,598,599),(600,601))),((602,603),604,605,(606,607,608,609),610),611,612,(613,614),(615,616),(((((617,618,619),(620,621,622,623)),624),((625,626,627,628,629,630,631,632,633,634),635)),636,((637,638,639,640,641,642,643),((644,645,646,647,648,649,650,651,652),(653,654))))),(655,656)),((657,(((658,659,660,661,662,663),((664,6 6 >5),666)),(((667,668,669,670,671,672,673,674),(675,676,677,678,679,680,681,682,683,684,685,686,687,688,689),690,(691,692,693,694,695)),((696,697),((698,699,700,701),(702,703,704,705)),(706,707,708,709,710))))),(711,712,713,714)))))))),(715,716,717,718,719))),((((((((((720,721,722,723,724,725,726,727),(728,729,730,731),732,(733,734),(735,736,737,738),(739,740),(741,742),743,(744,745,746,747,748,749),750,(751,752,753,754,755,756,757,758,759,760,761),(762,763),(764,765)),(((766,(767,768),((((((((769,((((((((770,(771,772)),(773,774)),((775,776),777)),(778,779)),780),781,782),(((783,784),785),(((((786,(787,788)),789),790),791),792))),793,(((((((((((794,795),(796,797)),798),(799,800)),801),(802,803)),(804,(805,806))),807),808),(((((((809,810),811),(812,813)),(814,815)),816),((817,818),819)),(((820,(821,822)),(823,824)),825))),826,827),(((((((((828,829),830),(831,832)),(833,834)),((835,836),837)),838,((839,840),841)),((842,843),844),845),(((846,(((847,848),849),850),851,852),853),(( 8 >54,(855,856)),(857,858)),(859,860,861),((((862,863),864),865),866))),867),((868,869),(870,871,872,((873,874),875),876,877)))),878,(879,880)),(881,882)),883),884),885),886),(887,888))),((889,(890,(891,892))),((893,894),((895,(896,897)),(898,899,900,901)))),902),903,904,((905,(906,907)),((908,909),(910,(911,912),913,914,915,(916,(917,918)),(919,920,(921,922,923),924),925,926)))),(((927,928),(929,930,931,(932,(933,934,935,936,937)))),938)),(939,940,941,942,943,(944,945),946,(947,948),(949,950),((((951,952),953),954),955,(956,957),(958,959),(960,961)),(962,963,((964,965),966,(967,968),969,(970,971))))),972,973,974),975),976),(977,978,979,(980,981))),(982,983)),(984,985)))); > >END; >Begin MESQUITE; > ??? > >setTreeNumber 1; > >setTree >'((1,2,3),(((((4,5,6,7,8,9,10),(11,12,13,14,15,16,17,18,19,20,21),(22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)),((((37,38),(39,40)),(41,((42,43),(((44,45),(46,47)),(48,49))))),50,((51,52,53),(54,55,56)))= 3 >)3 >,(((57,58,59,60),(((((61,62,63,(64,65)),((66,((67,68),69,(70,71,72,(73,74,75),76,77),(78,79,80,81,82,83,84,85,86,87),88,89,90,91,92,93,94,(95,96),97)),((98,99,100,101,102,103,104,105,106),(107,(108,109),110,111))),(((112,(113,114)),((115,116,117,118),(119,120,121,122,123)),(124,125),126),(((127,128,129,130,131,132,133,134,135,136,137,138),(139,140)),((141,142,143,144,145,146,147,148),(149,150,151,152,153,154,155))),156),(157,158),(((((159,160,161,162),163),((164,(((165,166),(167,168)),(169,170))),(171,172,173))),((174,175,176),(177,178)),(179,180,181,182),((183,(184,185)),186,187)),(188,((189,190,191,192,193,194,195),196))),(197,198),199,200,201),(202,(203,204,205,206),(207,((208,(209,210)),((211,212),((213,214),(215,216))))),((((217,218),((((219,220),221,222),(223,224),(225,226,227,228,229),(230,231),232,(233,234)),(235,236))),(237,(238,239),(((240,241),242),243))),(((244,245,246,247,248,249,250),(251,252,253,254,255,256,257,258,259,260,261,262,263,264,265)),266)),((267, 2 >68,269),270,271))),(272,273,274,275,276,277),(278,(279,280)),281),((282,283,284,285,286,287,288,289,290),(291,292))),(((293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323),(((324,325,326,327,328,329,330,331),(332,333)),(334,335,336,337,338,339,340,341,342))),((343,(344,345,346),(347,348),349,350,351,352,(353,354),355,356,(357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398)),(((399,400,401,402,403,404,405),(406,407,408,409,410,411)),(((412,413,414,415,416,417),(418,419,420,421,422,423,424,425,426,427),428),((((429,430),(431,432)),433,((((((434,435),(436,437)),(438,439,440,441,442,443,444,445,446,447,448,449,450)),(451,452,453,454,455,456,457,458),((459,460),461,462)),((463,464),((465,466,467,468,469,470,471,472,473,474),((((((475,(476,477,478,479,480,481,482,483,484,485,486,487,488,489,490 , >491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509)),(510,511)),(512,(513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533))),((534,535,536,537),(538,539,540,541= >14 >,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560))),(((561,562,563,564,565,566,567,568),569),570)= >14 >),571,572,573,574,575,(576,577),(578,579)),(580,581,582,583),584,585,(586,587,588,589,590,591,592,593,594,595))),(596,(597,598,599),(600,601))),((602,603),604,605,(606,607,608,609),610),611,612,(613,614),(615,616),(((((617,618,619),(620,621,622,623)),624),((625,626,627,628,629,630,631,632,633,634),635)),636,((637,638,639,640,641,642,643),((644,645,646,647,648,649,650,651,652),(653,654))))),(655,656)),((657,(((658,659,660,661,662,663),((664,665),666)),(((667,668,669,670,671,672,673,674),(675,676,677,678,679,680,681,682,683,684,685,686,687,688,689),690,(691,692,693,694,695)),((696,697),((698,699,700,701),(702,703,704,705)),(706,707,708,709,710))))),(711,712,713,714)))))))),(715,716,717,718,719))),((((((((((720,721,722,723,724,725,726,727),(728,729,730,731),732,(733,734),(735,736,737,738),(739,740),(741,742),743,(744,745,746,747,748,749),750,(751,752,753,754,755,756,757,758,759,760,761),(762,763),(764,765)),(((766,(767,768),((((((((769,((((((((770,(771,772)),(773,774)),((77 5 >,776),777)),(778,779)),780),781,782),(((783,784),785),(((((786,(787,788)),789),790),791),792))),793,(((((((((((794,795),(796,797)),798),(799,800)),801),(802= >3 >,803)),(804,(805,806))),807),808),(((((((809,810),811),(812,813)),(814,815)),816),((817,818),819)),(((820,(821,822)),(823,824)),825))),826,827),(((((((((828,829),830),(831,832= >14 >)),(833,834)),((835,836),837)),838,((839,840),841)),((842,843),844),845),(((846,(((847,848),849),850),851,852),853= >14 >),((854,(855,856)),(857,858)),(859,860,861),((((862,863),864),865),866))),867),((868,869),(870,871,872,((873,874),875),876,877)))),878,(879,880)),(881,882)),883),884),885),886),(887,888))),((889,(890,(891,892))),((893,894),((895,(896,897)),(898,899,900,901)))),902),903,904,((905,(906,907)),((908,909),(910,(911,912),913,914,915,(916,(917,918)),(919,920,(921,922,923),924),925,926)))),(((927,928),(929,930,931,(932,(933,934,935,936,937)))),938)),(939,940,941,942,943,(944,945),946,(947,948),(949,950),((((951,952),953),954),955,(956,957),(958,959),(960,961)),(962,963,((964,965),966,(967,968),969,(970,971))))),972,973,974),975),976),(977,978,979,(980,981))),(982,983)),(984,985))));'; > >Thanks sorry for two emails. >Daniel >_______________________________ >Daniel Hanley >PhD Candidate >Department of Biological Sciences >401 Sunset Avenue, Biology Building >University of Windsor >Windsor, Ontario, Canada, N9B 3P4 > >Phone: (519) 253-3000 ext 2704 >Fax: (519) 971-3609 >http://www.uwindsor.ca/hanleyd > >From: mesquitelist-bounces at mesquiteproject.org >[mailto:mesquitelist-bounces at mesquiteproject.org] On Behalf Of >Daniel Hanley >Sent: 2-October-09 1:59 PM >To: mesquitelist at mesquiteproject.org >Subject: [Mesquitelist] problem importing tree to R > >Dear Mail List Members, > I have been making a large phylogeny in Mesquite for >quite a while that no longer appears to import into R. I believe >this is an issue with the formatting in Mesquite and am looking for >guidance in how to export it so that it is readable by other >programs. The particular tree has close to 700 tips and some >polytomies. It also has colored branches, and annotated branches in >various spots within the tree). This has made the nexus code rather >sloppy. I've tried everything to get this to be read into R with >read.nexus function, but it dosen't appear to be. The formatting >stays in the nexus file despite the format it is exported as. It is >present even when I export as Phyllip. I also have tried manually >removing the clutter, but that didn't work either. The reason I >don't think it's an issue with R, is because it used to import this >tree, and it still imports a larger unformatted tree (~9,000 tips). >If anyone could give me some guidance I would greatly appreciate it. >Best, Daniel > >_______________________________ >Daniel Hanley >PhD Candidate >Department of Biological Sciences >401 Sunset Avenue, Biology Building >University of Windsor >Windsor, Ontario, Canada, N9B 3P4 > >Phone: (519) 253-3000 ext 2704 >Fax: (519) 971-3609 >http://www.uwindsor.ca/hanleyd > > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From wmaddisn at interchange.ubc.ca Mon Oct 5 20:49:46 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 05 Oct 2009 20:49:46 -0700 Subject: [Mesquitelist] PrinterException & StackOverflowError in Mesquite Message-ID: Thanks to all of you for reporting your crash errors using Mesquite's error reporting system. We are quite pleased that the system is showing us various crashes that probably went unreported in the past. We've been using the reports to fix bugs in NucleotideComplement, StateNamesEditor, and reading character matrices. We've noticed a series of checksum errors, but we will need to issue an update that will gather more information to help us understand that. If you've reported crash errors and would like help urgently, please write info at mesquiteproject.org. Otherwise we will fix the bugs as we solve them and will have an update ready in the next month or two. I'd like to ask for any help you can give about two errors that have been reported, PrinterException and StackOverflowError. PrinterException ========================= First, several of you using Windows have had the following error. java.awt.print.PrinterException: Invalid name of PrintService. A command could not be completed because an exception occurred (i.e. a crash; class java.awt.print.PrinterException ). WARNING: there is a chance this crash could have corrupted your data. Please check your data carefully. If you save any files, you might best use Save As... in case file saving doesn't work properly. sun.awt.windows.WPrinterJob.setNativePrintService(Native Method) sun.awt.windows.WPrinterJob.getPrintService(Unknown Source) sun.awt.windows.WPrinterJob.pageDialog(Unknown Source) mesquite.lib.MesquitePrintJob.preparePrint(Unknown Source) mesquite.lib.MesquitePrintJob.getPrintJob(Unknown Source) mesquite.lib.MesquiteWindow.prWindow(Unknown Source) mesquite.lib.MesquiteWindow.doCommand(Unknown Source) mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.doCommand(Unknown Source) mesquite.lib.PendingCommand.go(Unknown Source) mesquite.lib.MainThread.run(Unknown Source) This error seems to be not Mesquite's fault, but rather a bug in Java. However, we're not sure. For those of you who have experienced this problem, does it continue to happen if you go to another program or control panel and change default printers? Does it happen every time you try to print a tree? Does it happen if you try to print something else, e.g. a chart or matrix? What is your default printer? StackOverflowError ========================= Second, one of you had a StackOverflowError when using the Make All Rerootings tool. If you had this error, could you tell me off-list any more details? Most useful would be a data file and explicit instructions as to how to reproduce it. java.lang.StackOverflowError A command could not be completed because an error occurred (i.e. a crash; class java.lang.StackOverflowError ). WARNING: there is a chance this crash could have corrupted your data. Please check your data carefully. If you save any files, you might best use Save As... in case file saving doesn't work properly. mesquite.lib.MesquiteTree.totalBranchLength(Unknown Source) mesquite.lib.MesquiteTree.totalBranchLength(Unknown Source) mesquite.lib.MesquiteTree.totalBranchLength(Unknown Source) mesquite.lib.MesquiteTree.totalBranchLength(Unknown Source) mesquite.lib.MesquiteTree.totalBranchLength(Unknown Source) mesquite.lib.MesquiteTree.totalBranchLength(Unknown Source) mesquite.lib.MesquiteTree.totalBranchLength(Unknown Source) and so on. ============================ Thanks again for reporting crashes. Wayne -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From jonah.choiniere at gmail.com Fri Oct 9 10:12:50 2009 From: jonah.choiniere at gmail.com (Jonah Choiniere) Date: Fri, 9 Oct 2009 13:12:50 -0400 Subject: [Mesquitelist] stratigraphic tools (Laurin et al) issues Message-ID: All, I am wondering if anyone else has encountered issues when trying to add the stratigraphic tools modules to Mesquite v2.71. These modules worked in the previous version of Mesquite on my PC, but now they induce an error message when placed in the mesquite subfolder: Error while loading mesquite.assoc.stratigraphicPackages.stratigraphicPackages.modules.stratAdd.ExportTree.ExportTree. It appears that a component of Mesquite or a required library is missing. Details: java.lang.NoClassDefFoundError: mesquite/assoc/stratigraphicPackages/stratigraphicPackages/modules/stratAdd/ExportTree/ExportTree (wrong name: mesquite/stratAdd/ExportTree/ExportTree) I've successfully installed the modules on a Mac running Msq v2.5. Furthermore, the manual for Stratigraphic tools is only partially legible with a text editor, I can't seem to figure out what file format it is in. Sincerely, jonah -- Jonah Choiniere Ph.D. Candidate The George Washington University Robert Weintraub Program in Systematics and Evolution -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091009/bc45a010/attachment.html From wmaddisn at interchange.ubc.ca Fri Oct 9 12:28:28 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 09 Oct 2009 12:28:28 -0700 Subject: [Mesquitelist] stratigraphic tools (Laurin et al) issues In-Reply-To: References: Message-ID: It looks as if the modules are mis-installed. The error indicates you have the modules for stratAdd installed within a folder "modules", and that this is installed within assoc. Assoc is a built in package of Mesquite modules; other things should not be installed there. Try moving stratAdd so that it is directly within Mesquite_Folder/mesquite. You can then delete the folder stratigraphicPackages. Wayne At 1:12 PM -0400 9.10.2009, Jonah Choiniere wrote: >All, > >I am wondering if anyone else has encountered issues when trying to >add the stratigraphic tools modules to Mesquite v2.71. These modules >worked in the previous version of Mesquite on my PC, but now they >induce an error message when placed in the mesquite subfolder: > >Error while loading >mesquite.assoc.stratigraphicPackages.stratigraphicPackages.modules.stratAdd.ExportTree.ExportTree. > It appears that a component of Mesquite or a required library is >missing. > >Details: java.lang.NoClassDefFoundError: >mesquite/assoc/stratigraphicPackages/stratigraphicPackages/modules/stratAdd/ExportTree/ExportTree >(wrong name: mesquite/stratAdd/ExportTree/ExportTree) > > >I've successfully installed the modules on a Mac running Msq v2.5. > >Furthermore, the manual for Stratigraphic tools is only partially >legible with a text editor, I can't seem to figure out what file >format it is in. > > >Sincerely, >jonah > >-- >Jonah Choiniere >Ph.D. Candidate >The George Washington University >Robert Weintraub Program in Systematics and Evolution > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From wmaddisn at interchange.ubc.ca Fri Oct 9 14:31:31 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 09 Oct 2009 14:31:31 -0700 Subject: [Mesquitelist] stratigraphic tools (Laurin et al) issues In-Reply-To: References: Message-ID: The Stratigraphic tools manual is Microsoft Word format (the older style, .doc, not the newer .docx style). If you don't have Microsoft Word, I believe the free OpenOffice should be able to read the format. Wayne At 1:12 PM -0400 9.10.2009, Jonah Choiniere wrote: >All, > >I am wondering if anyone else has encountered issues when trying to >add the stratigraphic tools modules to Mesquite v2.71. These modules >worked in the previous version of Mesquite on my PC, but now they >induce an error message when placed in the mesquite subfolder: > >Error while loading >mesquite.assoc.stratigraphicPackages.stratigraphicPackages.modules.stratAdd.ExportTree.ExportTree. > It appears that a component of Mesquite or a required library is >missing. > >Details: java.lang.NoClassDefFoundError: >mesquite/assoc/stratigraphicPackages/stratigraphicPackages/modules/stratAdd/ExportTree/ExportTree >(wrong name: mesquite/stratAdd/ExportTree/ExportTree) > > >I've successfully installed the modules on a Mac running Msq v2.5. > >Furthermore, the manual for Stratigraphic tools is only partially >legible with a text editor, I can't seem to figure out what file >format it is in. > > >Sincerely, >jonah > >-- >Jonah Choiniere >Ph.D. Candidate >The George Washington University >Robert Weintraub Program in Systematics and Evolution > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From wmaddisn at interchange.ubc.ca Fri Oct 9 20:27:51 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 09 Oct 2009 20:27:51 -0700 Subject: [Mesquitelist] stratigraphic tools (Laurin et al) issues In-Reply-To: <722_1255123923_1255123923_a06240800c6f55ba15d17@[192.168.0.140]> References: <722_1255123923_1255123923_a06240800c6f55ba15d17@[192.168.0.140]> Message-ID: Jonah pointed out that the posted manual for StratigraphicTools could not be opened successfully with Microsoft Word. Michel Laurin has supplied a new copy, and I've replaced the manual in the download at http://mesquiteproject.org/packages/stratigraphicTools Wayne At 2:31 PM -0700 9.10.2009, Wayne Maddison wrote: >The Stratigraphic tools manual is Microsoft Word format (the older >style, .doc, not the newer .docx style). If you don't have Microsoft >Word, I believe the free OpenOffice should be able to read the format. > >Wayne > >At 1:12 PM -0400 9.10.2009, Jonah Choiniere wrote: >>All, >> >>I am wondering if anyone else has encountered issues when trying to >>add the stratigraphic tools modules to Mesquite v2.71. These modules >>worked in the previous version of Mesquite on my PC, but now they >>induce an error message when placed in the mesquite subfolder: >> >>Error while loading >>mesquite.assoc.stratigraphicPackages.stratigraphicPackages.modules.stratAdd.ExportTree.ExportTree. >> It appears that a component of Mesquite or a required library is >>missing. >> >>Details: java.lang.NoClassDefFoundError: >>mesquite/assoc/stratigraphicPackages/stratigraphicPackages/modules/stratAdd/ExportTree/ExportTree >>(wrong name: mesquite/stratAdd/ExportTree/ExportTree) >> >> >>I've successfully installed the modules on a Mac running Msq v2.5. >> >>Furthermore, the manual for Stratigraphic tools is only partially >>legible with a text editor, I can't seem to figure out what file >>format it is in. >> >> >>Sincerely, >>jonah >> >>-- >>Jonah Choiniere >>Ph.D. Candidate >>The George Washington University >>Robert Weintraub Program in Systematics and Evolution >> >>_______________________________________________ >>Mesquitelist mailing list >>Mesquitelist at mesquiteproject.org >>http://mesquiteproject.org/mailman/listinfo/mesquitelist > > >-- >-------------------------------------------------------- >Wayne Maddison > Professor and Canada Research Chair > Depts. of Zoology and Botany and > Biodiversity Research Centre > & Director > Beaty Biodiversity Museum > 6270 University Boulevard > University of British Columbia > Vancouver, BC V6T 1Z4 Canada > >email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 > >Mesquite: http://mesquiteproject.org >MacClade: http://macclade.org >Salticidae: http://salticidae.org >Tree of Life: http://tolweb.org >Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >Home page: http://salticidae.org/wpm/home.html >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From victor_dill at hotmail.com Thu Oct 15 11:56:02 2009 From: victor_dill at hotmail.com (Victor Dill) Date: Thu, 15 Oct 2009 15:56:02 -0300 Subject: [Mesquitelist] Bug on character groups Message-ID: Hi all, I believe that I have found a bug in Mesquite 2.71 related to group configurations. I have been grouping characteres according to my convinence, for instance, marking all characters related for a given structure. However, when I close the matrix for more than a few minutes, some characters -usually the same basic ones and some other eventually- when I re-open it, they present other configuratin, different from the one I assigned. Sometimes the original '?' and sometimes one other group. Best whishes to all, Victor _________________________________________________________________ Voc? sabia que o Hotmail mudou? Clique e descubra as novidades. http://www.microsoft.com/brasil/windows/windowslive/products/hotmail.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091015/505877f2/attachment.html From wmaddisn at interchange.ubc.ca Fri Oct 16 08:23:39 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 16 Oct 2009 08:23:39 -0700 Subject: [Mesquitelist] Bug on character groups In-Reply-To: References: Message-ID: Were there any reported errors during your work? To diagnose this, we need to understand the circumstances more precisely. Are you able to give step by step instructions that always make it happen? thanks, Wayne At 3:56 PM -0300 15.10.2009, Victor Dill wrote: >Hi all, > >I believe that I have found a bug in Mesquite 2.71 related to group >configurations. > >I have been grouping characteres according to my convinence, for >instance, marking all characters related for a given structure. > >However, when I close the matrix for more than a few minutes, some >characters -usually the same basic ones and some other eventually- >when I re-open it, they present other configuratin, different from >the one I assigned. Sometimes the original '?' and sometimes one >other group. > >Best whishes to all, >Victor > > > > >Voc? sabia que pode utilizar o Messenger de qualquer tipo de >celular? >Saiba >mais. > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From yy9 at rice.edu Mon Oct 19 13:32:17 2009 From: yy9 at rice.edu (yy9 at rice.edu) Date: Mon, 19 Oct 2009 15:32:17 -0500 Subject: [Mesquitelist] root a tree with an outgroup using script Message-ID: <20091019153217.20073s9f2nv426dc@webmail.rice.edu> Hi guys: I'm a new user of Mesquite. I met with a problem now and I hope anyone here can help me. I'm doing the simulation and I need to generate 500 trees with an outgroup using script. My problem is how to assign an outgroup in script. Is it using "getEmploy #mesquite.treefarm.OutgroupRoot.OutgroupRoot" and how to assign the outgroup? Following is the script I use to generate 1 tree. I appreciate if who can help me with how to add the feature of assigning the outgroup. Thanks! Yun #NEXUS BEGIN TAXA; TITLE species; DIMENSIONS NTAX=8; TAXLABELS A B C D E F G H ; END; BEGIN MESQUITECHARMODELS; CharModel gamma2 (Gamma) = shape = 0.8 discrete categories = 4; CharModel titv3 (RateMatrixTiTv) = tRatio = 3.0; CharModel AT0.6 (StateFrequencyUserSpecifiedDNA) = frequencies = (0.3 0.2 0.2 0.3) ; CharModel simple (DNASimulationModel) = 'setRootStatesModel AT0.6; setEquilStatesModel AT0.6; setCharRatesModel gamma2; setRateMatrixModel titv3; setScalingFactor 3.0E-8; '; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3663799439265828690; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3663799439265828690 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.SimulateTree.SimulateTree; tell It; setTreeSimulator #mesquite.trees.EqualRatesMarkovSp.EqualRatesMarkovSp; tell It; setTime 100000.0; endTell; setSeed 1958; endTell; setAssignedID 531.1038354825407.6738691587701733371; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.ArcTree.ArcTree; tell It; setEdgeWidth 8; orientUp; getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle on; toggleScale on; toggleCenter on; toggleEven on; namesAngle ?; endTell; endTell; setBackground White; setBranchColor Blue; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleNodeLabels on; toggleShowNames on; endTell; endTell; getTreeWindow; tell It; setSize 787 540; setLocation 326 22; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 30; setAnnotationSize 20; getToolPalette; tell It; endTell; setTreeNumber 1; toggleSizeToFit on; toggleTextOnTree off; endTell; showWindow; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; endTell; endTell; endTell; end; From gzehender at gmail.com Tue Oct 20 05:24:31 2009 From: gzehender at gmail.com (Gianguglielmo Zehender) Date: Tue, 20 Oct 2009 14:24:31 +0200 Subject: [Mesquitelist] slatkin maddison test help Message-ID: <9f8a6f230910200524i1794f9f1x53a5eefca0912409@mail.gmail.com> Hi all, I am new in using Slatkin Maddison's test and I have some doubts. I am trying to test the compartmentalization of my taxa. When I simulate trees to evaluate the s distribution, how I can estimate the poulation size? It is correct to use the N0 estimate by coalescent approach (using Beast program) under a constant growth model? How many trees shuld be simulated to be confident in the result? (1000 or more?). Finally, in an analysis I estimated s=6 for my gene-tree and a distribution of s between 9 and 15 (considering 95% trees). What does it means? 1. My tree is not included in the 95% of the simulated tree, so it doesn't support compartmentalization; or 2. The number of migrations in my tree is lower than that estimated by simulation, so my tree support the compartmentalization....[?] Help me, please. Thank you. Gianni -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091020/07c29c67/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 226 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091020/07c29c67/attachment.gif From wmaddisn at interchange.ubc.ca Wed Oct 21 13:18:48 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Wed, 21 Oct 2009 13:18:48 -0700 Subject: [Mesquitelist] Java crashes with Mesquite Message-ID: Some of you have reported crashes in which Mesquite simply quits or vanishes. On Windows, a message about an unexpected error may appear; on OS X a notice about an application unexpectedly quitting may appear. These crashes reflect bugs in Java itself, not in Mesquite. These crashes are different from the ones in which Mesquite indicates an Exception or Error occured and puts up a dialog box. The crashes we'd like to know about here are the ones in which Mesquite spontaneously quits. Could any of you who have such crashes please send me an email? We would like to know how often they happen, and anything you can tell us about them. Thanks, Wayne -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html