User: Wilber0x

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Wilber0x10
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Posts by Wilber0x

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Biopython - AttributeError: when downloading from genbank
... This was the problem, thanks for the help! ...
written 29 days ago by Wilber0x10
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Comment: C: Biopython - AttributeError: when downloading from genbank
... I have tried increasing the delay to 60s, and got the same number downloaded as when I used a 1.5s delay. Perhaps I should just do it in batches of 140 rather than all at once. ...
written 29 days ago by Wilber0x10
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Comment: C: Biopython - AttributeError: when downloading from genbank
... I used an Entrez API key, and have incorporated delays into my script. Whether the delay is 1.5s or 60s between requests, I still get the same error after 150 plastid genomes. ...
written 29 days ago by Wilber0x10
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Comment: C: Biopython - AttributeError: when downloading from genbank
... I have built in a time delay upon your suggestion so only one query is submitted per second. This improves the number of sequences downloaded to 140, but still results in the same error message. ...
written 4 weeks ago by Wilber0x10
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Comment: C: Biopython - AttributeError: when downloading from genbank
... Thank you for your help ...
written 4 weeks ago by Wilber0x10
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Biopython - AttributeError: when downloading from genbank
... I have a list of around 200 plastid genomes which I want to download from genbank using biopython, and then put into one .gb file. Here is the code I am using to do this: out_handle = open(filename, "w") for i in range(len(genbankIDs)): net_handle = Entrez.efetch( db="nucleot ...
software error biopython written 4 weeks ago by Wilber0x10 • updated 4 weeks ago by Shred230
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Use mesquite to make a supertree
... Has anyone used mesquite to create a supertree? I have two phylogenetic trees, one of genera, and one for a specific genus. I would like to replace the tip for the genus on my tree of genera with my more fine level phylogeny of species. The branch lengths do not matter, as I only need a way to disp ...
phylogeny genome phylogenetics alignment sequence written 11 weeks ago by Wilber0x10
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Comment: C: Software to allow manual adding of branches to to phylogenetic tree
... I phrased my question incorrectly, I want to add branches manually to a cladogram. The relationships between the species I am interested in are already known, I simply want to map some characters on to the cladogram. Thank you for your help. ...
written 3 months ago by Wilber0x10
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Software to allow manual adding of branches to to phylogenetic tree
... I have a phylogenetic tree, and I would like to add some branches into it manually. Does anyone know of any software that would allow me to do this using a GUI, rather than editing nexus files manually? I cannot find a way to do this in mesquite. ...
genome phylogeny phylogenetics evolution written 3 months ago by Wilber0x10 • updated 3 months ago by Mensur Dlakic7.1k
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RAxML generate best tree from 500 bootstrap trees
... I am using RAxML. I want to make a single maximum likelihood tree based on 500 boostraps. I am also using partitions for my alignment. I used this command in RAxML: raxmlHPC-PTHREADS-AVX2 -m GTRGAMMA -p $RANDOM -x $RANDOM -N 500 -T 4 -s myAlignment.phy -q partitionSchemel.txt -n output.tre I ...
sequence phylogenetics raxml written 5 months ago by Wilber0x10 • updated 5 months ago by ugurcabuk130

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For alignment of multiple multifasta files- MAFFT command line

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