Hello!!
I have a similar problem and I am trying to solve it. I tried the two for-loops you suggested, but I think I get an error on the first file and then I am thrown outside the loop and everything stops there. See below what I do and what I get:
for subdirectory in .; do for file in $subdirectory; do raxmlHPC -m GTRGAMMA -p 12345 -s $file -b 12345 -#100 -T 2 -n tree; done; done
Use raxml with AVX support with overriden number of threads
RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file
TOO FEW SPECIES
It is probably something wrong in my loop but my brain is stuck right now...
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katerinapargana •
why not concatenate all alignments together? As I know, concatenation is a standard approach in multi-locus phylogeny reconstruction. Maybe you have different Taxon sampling in each alignment?
Thank you for the reply. I think concatenating the sequences would produce an accurate tree and I will do that; however, a few recent publications are big on using many trees to create a consensus tree and I wanted to try it out as well. I do not know how much they will vary. I'll continue posting what I learn to this thread.
I think you're talking about the supertree approaches. Usually they're used when taxon sampling can't be matched for each locus and you'd like to keep as much as information as possible (concatenation would throw away alignments that have missing taxa).
My bacteria are especially adept at lateral gene transfer so you're correct that not every strain matched locus for locus. It would be nice to retain as much data as possible in the tree.
Lateral gene transfer is a major problem in phylogeny reconstruction of prokaryotes. Indeed, supertree methods might be better in this case, to resolve the lateral gene transfers where you see strong topology disagree among loci.