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Believe I have it all set up properly, but when I run the test as shown, it fails at the phylip step:
python alfie.py -v -r test/homo_y.fasta -i test/pan_y.fasta -g test/y.gtf
starting al_finder
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I may be misunderstanding, but is there a way to convert long sequences like chromosomes from hal to fasta or phylip multiple alignment formats? I've tried cactus-hal2maf and then various maf 2 fasta …
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Hi Sungsik,
Thank you for creating this program. I would love to try it out but I am having some troubles uploading my sequential phylip file.
Here is what the first few lines look like.
86 …
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Might be good to pass to quicktree and rapidnj
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Hello,
I would like more information on the encoding of the phylip output. Let's say that the reference allele at one alignment position is C. What happens if, at this alignment position:
1. There…
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Hello. It says that vcf2pop exports a Phylip file although, I do not see any outputted file. How do I get the diversity matrix off of the html website so it can be used with phangorn?
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Dear seqinr team
I have a request.
I am designing PCRs for different phylogenetic levels based on a few hundred sequences. For that purpose it had been handy to have a consensus sequence with IU…
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Hi,
I used MAFFT for multiple alignments of the whole genome. However, it generates a fasta format. When I use this fast format alignment file, RAxML uses only one thread instead of multiple threads…
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I am having some trouble with PHYLIP on my computer, what is the path to access it on PACE? I think it may be easier at this point just to transfer my files to and from the cluster. Thanks!
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Other formats work, but not phylip for some raisin:
```
josephwb@Potiphar-Breen:baits$ cat foo.fa | pxlssq
File type: fasta
Number of sequences: 4568
Is aligned: true
Sequence length: 2571
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