User: shadowstep

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shadowstep0
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Posts by shadowstep

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Comment: C: How to simplify phylip file headings
... I'm not familiar with this command, could you please explain more? ...
written 4 months ago by shadowstep0
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Comment: C: How to simplify phylip file headings
... Thanks, I tried the script in windows powershell, now I'm going to install pycharm to dive into python deeper ...
written 4 months ago by shadowstep0
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Comment: C: How to simplify phylip file headings
... Perhaps it is not capable of simplifying interleaved alignment, this script gave me an list index out of range error, ...
written 4 months ago by shadowstep0
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How to simplify phylip file headings
... Suppose I have a phylip alignment like: (I should mention that it is interleaved) KM894618.1_Abutilon_oxycarpum_voucher_1076420545_maturase_K_(matK)_gene_partial_cds_chloroplast --------------------------------TCTTTGCATTTATTACGGTTCTCTCTCT KU508975.1_Acalypha_austr ...
phylip written 4 months ago by shadowstep0 • updated 4 months ago by finswimmer6.2k
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Is it possible to assess similarity between two phylo trees?
... In a recent paper, the authors concluded that the topology of their tree is very similar to a previous study, giving P < 0.001 and ρ = 0.947. I think it could be a correlation test, but I don't know how to achieve this. Can I do this in R? What package/function should I use? ...
phylogeny written 4 months ago by shadowstep0 • updated 4 months ago by Frank Wright (BioSS)0
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How to root a phylogenetic tree when calculating phylogenetic diversity in plant community?
... I randomly draw some species (say 1, 2 and 4) from a 8 common species pool to assemble the communities, then transplant a special species X into the communities. Now I want to measure the effect of phylogenetic diversity of the communities, on the growth performance of species X. Q1: I first estima ...
phylogeny written 5 months ago by shadowstep0
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Substitution model testing tool for linux command line
... Mega 7 has a function to find best DNA models, it will give a complete analyze table with parameters In linux command line, is there a package that can do this job? I want to validate the results from Mega. Thank you. ...
substitution model written 6 months ago by shadowstep0 • updated 6 months ago by h.mon20k
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Comment: C: How to derive phylo tree from two genes
... I think I've got the point, if I don't do bootstrap, then the auto-generated best tree is actually the best, and indeed bootstrapping is intended to gauge nodal support, am I right? ...
written 6 months ago by shadowstep0
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Comment: C: How to derive phylo tree from two genes
... 1000 is too complicated for my computer though. I calculated 100 bootstraps using RAxML command line, but I don't know how to get this best tree, I searched a lot but found nothing ...
written 6 months ago by shadowstep0
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Comment: C: How to derive phylo tree from two genes
... Thank you, one more question, when calculating phylo tree through maximum likelihood estimation, can I summarize a "best" tree from 100 bootstraps? ...
written 6 months ago by shadowstep0

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