Editing phylogenetic data matrices for use in PAUP and TNT

[@QT5656]

Many thanks Rob!

[@robertasher9639]

around 16:58 I mistakenly say that "there aren't more than 8 states" but in fact there are (0-5 morph, acgt dna). However nstates 8 still works because for this (very small) subset of taxa from Huttenlocker et al. 2018, some of the states are uninformative & none are additive. Type "nstates?" at the TNT prompt or see phylo.wikidot.com/tntwiki

[@FilipD-fx1kd]

I have a question, how to create a matrix from characteristics, such as for example, lack of white flowers - 0, white flowers - 1, and put it into PAUP?

[@QT5656]

11:12 for TNT

[@danielnakamura6430]

How would you create a matrix for continuous characters?

[@robertasher9639]

There's a literature on this. E.g., have a look at these papers on the subject of continuous characters: Goloboff PA, Mattoni CI, Quinteros AS. Continuous characters analyzed as such. Cladistics. 2006 Dec;22(6):589-601. and Parins-Fukuchi C. Use of continuous traits can improve morphological phylogenetics. Systematic Biology. 2018 Mar 1;67(2):328-39.

[@imranfakhar2807]

@@robertasher9639 can you make a video about it too?

[@imranfakhar2807]

@@robertasher9639 I am trying to learn gap weighting for continuous characters but I didn't able to do that

[@fabriciomoreiraferreira8199]

Dear Robert Asher. I'm Fabrício, from Brazil. I'm tring to run a combined analyses (DNA + morphological data). However, I'm not sure if my data Block and command block are correct. Can you check my commands, please? Cheers BEGIN DATA; DIMENSIONS NTAX=45 NCHAR=1782; [ITS1=159; 5.8S=185; ITS2=341; rpl32gene=146; rpl32-trnlspacer-trnlgene=898; Morphology=53]; FORMAT DATATYPE = DNA [(STANDARD:1-53, DNA:54-1782)] INTERLEAVE RESPECTCASE GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7"; OPTIONS GAPMODE=MISSING; BEGIN sets; Charset Standard=1-53;[53] Charset ITS1=54-212;[159] Charset 58S=213-397;[185] Charset ITS2=398-738;[341] Charset rpl32gene=739-884;[146] Charset rpl32trnlspacertrnlgene=885-1782;[898] END; begin assumptions; charset coding = 213-397 739-884; charset noncoding = 1-159 344-685 832-1709; charset standard = 1-53; charpartition gfunc = 1:coding, 2:noncoding; charset 1stpos = 213-397\3 739-884\3; charset 2ndpos = 214-397\3 740-884\3; charset 3rdpos = 215-397\3 741-884\3;

[@robertasher9639]

You'll have to run this yourself and base any corrections you make on the (usually informative) error messages you get. I'm not going to run your script for you. Having said that, keep in mind that MrBayes and PAUP nexus commands are not identical. If you're running this in paup then check your syntax, etc. with the docs from PAUP and not MrBAyes.

[@fabriciomoreiraferreira8199]

@@robertasher9639 ok

[@fabriciomoreiraferreira8199]

@@robertasher9639 thanks