User: shadowstep

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shadowstep0
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Posts by shadowstep

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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 8 days ago by shadowstep0 • updated 8 days ago by h.mon13k
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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 8 days 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 8 days 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 8 days ago by shadowstep0
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Comment: C: How to derive phylo tree from two genes
... Hi lieven.sterck, I'm going to calculate phylogenetic diversity of a plant community, maybe what I need is a species tree. Is there any command line tool available? ...
written 8 days ago by shadowstep0
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How to derive phylo tree from two genes
... I did multiple align for two genes, and got two multiple alignment files, each has nine sequences of the same nine species, for simplicity, I illustrate an example with 3 sequences. Alignent 1 : X AGCCTC Y ACCCTC Z ACGGTC Alignent 2: X CGGCATCC Y ...
alignment written 8 days ago by shadowstep0
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Can IGV visualize clustal format alignment?
... I produced a multiple alignment using mafft --clustalout seq.fasta > align.fa Is there any tool to help visualize this alignment file? IGV user guide said that a BAM file is required, how could I produce BAM format alignment file? Thank you! ...
igv written 9 days ago by shadowstep0 • updated 9 days ago by Ram14k
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How to concatenate two fasta files, using regular expressions
... ** Thanks for your answers, my dear colleagues, it seems that I can't click that reply button ** I have 2 sets of fasta sequences, they are actually 2 genes of 9 species. I put the sequences of 9 species of the same gene into one folder, and the other gene into another folder. Now I want to concate ...
fasta concatenate written 10 days ago by shadowstep0
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Comment: C: The procedures before calculating phylogenetic diversity of a plant community
... Thanks a lot @cschu181 ...
written 13 days ago by shadowstep0
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The procedures before calculating phylogenetic diversity of a plant community
... Hi, I'm new to molecular ecology and Biostars. Please don't mind that I have such a stupid question. For example, I have a plant community with 8 plant species. I downloaded matK and rbcL sequences for all 8 species from NCBI, respectively, in FASTA format. Therefore I have 2 x 8 sequences. Now I ...
phylogeny written 14 days ago by shadowstep0

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