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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, thanks for developing this tool
I run the script of vcf2phylip.py successfully but found the output seems to be the amino acid sequences. My code and the screenshort of my output file are as fo…
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Hi! I'm writing with a question about input matrix size limits. I have a large alignment file-- 158 individuals, 49M sites, and I'm getting a segmentation fault error. Do you have any recommendations …
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Hi,
The alignment is very fast in my case, which is based on one chromosome from different species. Thanks for the great work. I am going to build a phylogenetic tree with the alignments. So I used…
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Hello,
As the tite suggests i am trying to restart a run using the --resume flag as i had to stop my inital run on a HPC. I am confused as to what the resume flag needs to restart the run? I am cu…
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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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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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Hi,
I am running into following error while running treesub on a server.
[1/6] Copying file from '/home/my/data.fasta' to '/home/my/alignment'.
Successfully copied file.
[2/6] Converting FAST…
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the phyluce_align_format_nexus_files_for_raxml not works for phylip in this code
phyluce_align_concatenate_alignments \
--alignments mafft-gblocks-70p \
--output mafft-gblock…
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Minor suggestion, it might be good to change the wording of the file input prompt on the TreeScaper-CRA page to something other than "Collection of PHYLIP files". PHYLIP is just one of the many file …