Re: [MORPHMET] Phylogenetic tree in MorphoJ-regrading
Dear Arvind, MorphoJ allows you to map shape variation across multiple taxa onto an existing phylogenetic tree. So, you need to either use a published phylogeny of your taxa (e.g. accessioned in TreeBASE or Dryad, or from the authors) or reconstruct your own phylogenetic hypothesis of evolutionary relationships among your focal taxa. After you have one or multiple appropriate phylogenetic trees, you can then import them into MorphoJ (e.g. from a single NEXUS file), so long as there are no negative branch lengths or other formatting issues. Here is a link to the section of the MorphoJ documentation on the topic, which includes examples of NEXUS format accepted by the program: http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?file/ImpPhylogeny.htm Good luck with your analysis. Best, Justin Justin C. Bagley, Ph.D. Postdoctoral Research Associate Department of Biology University of Missouri-St. Louis One University Boulevard, 223 Research Building St. Louis, MO 63121-4499 E-mail: bagl...@umsl.edu Website: https://justinbagley.org CV: https://justinbagley.org/pages/cv.html Blog: https://justinbagley.rbind.io Affiliate Researcher Department of Biology Virginia Commonwealth University 1000 W Cary St, Rm 126, Richmond, VA 23284-2012 On Mon, Jan 28, 2019 at 11:07 AM Arvind Kumar Dwivedi wrote: > Dear Sir/Ma'am > > Greetings... > > I am working on shape variations among fishes. > > I have a problem in preparing phylogenetic tree in MorphoJ software. > > MorphoJ is asking to upload NEXUS file to prepare phylogenetic tree. > > I have two major queries: > > 1. Do I have to prepare NEXUS file from the 2D XY coordinate data ??? > > 2. If this is the case, how I can prepare NEXUS file I don not how to > format 2D XY data in NEXUS file. > > Here is my data on 2D XY coordinate for 3 species having 3 samples in each > species: > > LM=13 > 122.0 583.0 > 430.0 725.0 > 808.0 778.0 > 1083.0 748.0 > 1653.0 612.0 > 1706.0 523.0 > 1651.0 452.0 > 1489.0 462.0 > 1239.0 361.0 > 843.0 280.0 > 510.0 412.0 > 530.0 467.0 > 263.0 567.0 > IMAGE=TIL 845.JPG > ID=species1 > SCALE=0.013768 > LM=13 > 144.0 810.0 > 455.0 970.0 > 828.0 1024.0 > 1108.0 985.0 > 1665.0 862.0 > 1712.0 770.0 > 1651.0 692.0 > 1482.0 704.0 > 1264.0 594.0 > 861.0 550.0 > 538.0 658.0 > 562.0 722.0 > 303.0 803.0 > IMAGE=TIL 846.JPG > ID=species1 > SCALE=0.011780 > LM=13 > 75.0 935.0 > 436.0 1098.0 > 842.0 1140.0 > 1099.0 1092.0 > 1681.0 990.0 > 1735.0 902.0 > 1655.0 836.0 > 1521.0 819.0 > 1298.0 704.0 > 843.0 615.0 > 485.0 755.0 > 520.0 822.0 > 237.0 915.0 > IMAGE=TIL 847.JPG > ID=species1 > SCALE=0.014137 > LM=13 > 43.0 3131.0 > 110.0 3183.0 > 248.0 3212.0 > 316.0 3203.0 > 550.0 3182.0 > 573.0 3154.0 > 553.0 3123.0 > 497.0 3122.0 > 433.0 3089.0 > 282.0 3046.0 > 147.0 3072.0 > 149.0 3115.0 > 78.0 3138.0 > IMAGE=TIL 402.JPG > ID=species2 > SCALE=0.037037 > LM=13 > 83.0 3174.0 > 165.0 3222.0 > 278.0 3246.0 > 339.0 3238.0 > 549.0 3209.0 > 568.0 3175.0 > 546.0 3153.0 > 502.0 3162.0 > 434.0 3127.0 > 302.0 3100.0 > 193.0 3122.0 > 197.0 3158.0 > 132.0 3178.0 > IMAGE=TIL 403.JPG > ID=species2 > SCALE=0.038462 > LM=13 > 84.0 3126.0 > 155.0 3174.0 > 291.0 3205.0 > 347.0 3198.0 > 581.0 3154.0 > 597.0 3119.0 > 587.0 3096.0 > 522.0 3099.0 > 450.0 3066.0 > 304.0 3048.0 > 191.0 3077.0 > 195.0 3107.0 > 126.0 3135.0 > IMAGE=TIL 404.JPG > ID=species2 > SCALE=0.037037 > LM=13 > 45.0 1452.0 > 227.0 1601.0 > 478.0 1672.0 > 635.0 1656.0 > 1061.0 1568.0 > 1106.0 1508.0 > 1070.0 1452.0 > 840.0 1392.0 > 566.0 1317.0 > 338.0 1341.0 > 286.0 1320.0 > 177.0 1472.0 > 91.0 1469.0 > IMAGE=HKL 14.JPG > ID=species3 > SCALE=0.014700 > LM=13 > 68.0 1477.0 > 260.0 1605.0 > 494.0 1652.0 > 640.0 1627.0 > 1036.0 1529.0 > 1097.0 1467.0 > 1037.0 1418.0 > 805.0 1358.0 > 541.0 1316.0 > 344.0 1355.0 > 296.0 1332.0 > 203.0 1494.0 > 120.0 1492.0 > IMAGE=HKL 15.JPG > ID=species3 > SCALE=0.015385 > LM=13 > 56.0 1496.0 > 242.0 1620.0 > 506.0 1666.0 > 666.0 1645.0 > 1094.0 1532.0 > 1141.0 1471.0 > 1074.0 1423.0 > 835.0 1364.0 > 574.0 1315.0 > 341.0 1355.0 > 282.0 1341.0 > 175.0 1508.0 >
Re: [MORPHMET] Phylogenetic tree in MorphoJ-regrading
Arvind, The NEXUS format is used to represent phylogenetic trees, on which MorphoJ will map your shapes. You don't prepare 2D data in NEXUS format, as the software does not compute phylogenetic trees itself, See the MorphoJ documentation ( http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?index.htm), specifically the item "Comparison Menu" -> "Map Onto Phylogeny" for details. By the way, a comprehensive description of the NEXUS format can be found in the fine paper by Madison et al (1997): David R. Maddison, David L. Swofford, Wayne P. Maddison. " NEXUS: An Extensible File Format for Systematic Information". Systematic Biology, Vol. 46, No. 4 (Dec., 1997), pp. 590-621. Hope this helps. Best wishes, Em seg, 28 de jan de 2019 às 15:07, Arvind Kumar Dwivedi < dubeyma...@gmail.com> escreveu: > Dear Sir/Ma'am > > Greetings... > > I am working on shape variations among fishes. > > I have a problem in preparing phylogenetic tree in MorphoJ software. > > MorphoJ is asking to upload NEXUS file to prepare phylogenetic tree. > > I have two major queries: > > 1. Do I have to prepare NEXUS file from the 2D XY coordinate data ??? > > 2. If this is the case, how I can prepare NEXUS file I don not how to > format 2D XY data in NEXUS file. > > Here is my data on 2D XY coordinate for 3 species having 3 samples in each > species: > > LM=13 > 122.0 583.0 > 430.0 725.0 > 808.0 778.0 > 1083.0 748.0 > 1653.0 612.0 > 1706.0 523.0 > 1651.0 452.0 > 1489.0 462.0 > 1239.0 361.0 > 843.0 280.0 > 510.0 412.0 > 530.0 467.0 > 263.0 567.0 > IMAGE=TIL 845.JPG > ID=species1 > SCALE=0.013768 > LM=13 > 144.0 810.0 > 455.0 970.0 > 828.0 1024.0 > 1108.0 985.0 > 1665.0 862.0 > 1712.0 770.0 > 1651.0 692.0 > 1482.0 704.0 > 1264.0 594.0 > 861.0 550.0 > 538.0 658.0 > 562.0 722.0 > 303.0 803.0 > IMAGE=TIL 846.JPG > ID=species1 > SCALE=0.011780 > LM=13 > 75.0 935.0 > 436.0 1098.0 > 842.0 1140.0 > 1099.0 1092.0 > 1681.0 990.0 > 1735.0 902.0 > 1655.0 836.0 > 1521.0 819.0 > 1298.0 704.0 > 843.0 615.0 > 485.0 755.0 > 520.0 822.0 > 237.0 915.0 > IMAGE=TIL 847.JPG > ID=species1 > SCALE=0.014137 > LM=13 > 43.0 3131.0 > 110.0 3183.0 > 248.0 3212.0 > 316.0 3203.0 > 550.0 3182.0 > 573.0 3154.0 > 553.0 3123.0 > 497.0 3122.0 > 433.0 3089.0 > 282.0 3046.0 > 147.0 3072.0 > 149.0 3115.0 > 78.0 3138.0 > IMAGE=TIL 402.JPG > ID=species2 > SCALE=0.037037 > LM=13 > 83.0 3174.0 > 165.0 3222.0 > 278.0 3246.0 > 339.0 3238.0 > 549.0 3209.0 > 568.0 3175.0 > 546.0 3153.0 > 502.0 3162.0 > 434.0 3127.0 > 302.0 3100.0 > 193.0 3122.0 > 197.0 3158.0 > 132.0 3178.0 > IMAGE=TIL 403.JPG > ID=species2 > SCALE=0.038462 > LM=13 > 84.0 3126.0 > 155.0 3174.0 > 291.0 3205.0 > 347.0 3198.0 > 581.0 3154.0 > 597.0 3119.0 > 587.0 3096.0 > 522.0 3099.0 > 450.0 3066.0 > 304.0 3048.0 > 191.0 3077.0 > 195.0 3107.0 > 126.0 3135.0 > IMAGE=TIL 404.JPG > ID=species2 > SCALE=0.037037 > LM=13 > 45.0 1452.0 > 227.0 1601.0 > 478.0 1672.0 > 635.0 1656.0 > 1061.0 1568.0 > 1106.0 1508.0 > 1070.0 1452.0 > 840.0 1392.0 > 566.0 1317.0 > 338.0 1341.0 > 286.0 1320.0 > 177.0 1472.0 > 91.0 1469.0 > IMAGE=HKL 14.JPG > ID=species3 > SCALE=0.014700 > LM=13 > 68.0 1477.0 > 260.0 1605.0 > 494.0 1652.0 > 640.0 1627.0 > 1036.0 1529.0 > 1097.0 1467.0 > 1037.0 1418.0 > 805.0 1358.0 > 541.0 1316.0 > 344.0 1355.0 > 296.0 1332.0 > 203.0 1494.0 > 120.0 1492.0 > IMAGE=HKL 15.JPG > ID=species3 > SCALE=0.015385 > LM=13 > 56.0 1496.0 > 242.0 1620.0 > 506.0 1666.0 > 666.0 1645.0 > 1094.0 1532.0 > 1141.0 1471.0 > 1074.0 1423.0 > 835.0 1364.0 > 574.0 1315.0 > 341.0 1355.0 > 282.0 1341.0 > 175.0 1508.0 > 103.0 1513.0 > IMAGE=HKL 16.JPG > ID=species3 > SCALE=0.014284 > > Kindly suggest. > Desperately waiting for response from the experts. > > regards > Arvind > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- Dr. Mauro J. Cavalcanti
[MORPHMET] Phylogenetic tree in MorphoJ-regrading
Dear Sir/Ma'am Greetings... I am working on shape variations among fishes. I have a problem in preparing phylogenetic tree in MorphoJ software. MorphoJ is asking to upload NEXUS file to prepare phylogenetic tree. I have two major queries: 1. Do I have to prepare NEXUS file from the 2D XY coordinate data ??? 2. If this is the case, how I can prepare NEXUS file I don not how to format 2D XY data in NEXUS file. Here is my data on 2D XY coordinate for 3 species having 3 samples in each species: LM=13 122.0 583.0 430.0 725.0 808.0 778.0 1083.0 748.0 1653.0 612.0 1706.0 523.0 1651.0 452.0 1489.0 462.0 1239.0 361.0 843.0 280.0 510.0 412.0 530.0 467.0 263.0 567.0 IMAGE=TIL 845.JPG ID=species1 SCALE=0.013768 LM=13 144.0 810.0 455.0 970.0 828.0 1024.0 1108.0 985.0 1665.0 862.0 1712.0 770.0 1651.0 692.0 1482.0 704.0 1264.0 594.0 861.0 550.0 538.0 658.0 562.0 722.0 303.0 803.0 IMAGE=TIL 846.JPG ID=species1 SCALE=0.011780 LM=13 75.0 935.0 436.0 1098.0 842.0 1140.0 1099.0 1092.0 1681.0 990.0 1735.0 902.0 1655.0 836.0 1521.0 819.0 1298.0 704.0 843.0 615.0 485.0 755.0 520.0 822.0 237.0 915.0 IMAGE=TIL 847.JPG ID=species1 SCALE=0.014137 LM=13 43.0 3131.0 110.0 3183.0 248.0 3212.0 316.0 3203.0 550.0 3182.0 573.0 3154.0 553.0 3123.0 497.0 3122.0 433.0 3089.0 282.0 3046.0 147.0 3072.0 149.0 3115.0 78.0 3138.0 IMAGE=TIL 402.JPG ID=species2 SCALE=0.037037 LM=13 83.0 3174.0 165.0 3222.0 278.0 3246.0 339.0 3238.0 549.0 3209.0 568.0 3175.0 546.0 3153.0 502.0 3162.0 434.0 3127.0 302.0 3100.0 193.0 3122.0 197.0 3158.0 132.0 3178.0 IMAGE=TIL 403.JPG ID=species2 SCALE=0.038462 LM=13 84.0 3126.0 155.0 3174.0 291.0 3205.0 347.0 3198.0 581.0 3154.0 597.0 3119.0 587.0 3096.0 522.0 3099.0 450.0 3066.0 304.0 3048.0 191.0 3077.0 195.0 3107.0 126.0 3135.0 IMAGE=TIL 404.JPG ID=species2 SCALE=0.037037 LM=13 45.0 1452.0 227.0 1601.0 478.0 1672.0 635.0 1656.0 1061.0 1568.0 1106.0 1508.0 1070.0 1452.0 840.0 1392.0 566.0 1317.0 338.0 1341.0 286.0 1320.0 177.0 1472.0 91.0 1469.0 IMAGE=HKL 14.JPG ID=species3 SCALE=0.014700 LM=13 68.0 1477.0 260.0 1605.0 494.0 1652.0 640.0 1627.0 1036.0 1529.0 1097.0 1467.0 1037.0 1418.0 805.0 1358.0 541.0 1316.0 344.0 1355.0 296.0 1332.0 203.0 1494.0 120.0 1492.0 IMAGE=HKL 15.JPG ID=species3 SCALE=0.015385 LM=13 56.0 1496.0 242.0 1620.0 506.0 1666.0 666.0 1645.0 1094.0 1532.0 1141.0 1471.0 1074.0 1423.0 835.0 1364.0 574.0 1315.0 341.0 1355.0 282.0 1341.0 175.0 1508.0 103.0 1513.0 IMAGE=HKL 16.JPG ID=species3 SCALE=0.014284 Kindly suggest. Desperately waiting for response from the experts. regards Arvind -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
