User: jan

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jan0
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Posts by jan

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Fast site removal
... No, this is very cumbersome as I would have to find all the different thresholds to use by myself etc. Anyway, thanks for your suggestions. ...
written 5 months ago by jan0
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Comment: C: Fast site removal
... Thanks, but how is this removing sites from the alignment? ...
written 5 months ago by jan0
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Fast sites removal from alignment
... Hi all, I have a file listing site-specific substitution rates (file.rate; please see below). In several steps (à 4,000 sites), I would like to remove the fastest evolving sites (shown in column "Rate") from my AA alignment (file.ali). I would be very happy and grateful if you could help out (maybe ...
alignment sequence written 5 months ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... This is a great advice. Thank you very much! I had to replace "grep -wf - *.fa" by "grep -wf *.fa". I assume the dash was added accidentally, is that right? With the dash it wasn't working. However, now it's working but for all OTUs (headers), the number of files in which they are represented is r ...
written 10 months ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... Great, the edited version is doing the job :) Thank you, Pierre! ...
written 11 months ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... I am getting a long list showing the number of headers, which are shared among two files each. Getting the names of the 10 files with the most shared headers remains unresolved. Anyway, thanks for trying! ...
written 11 months ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... @Pierre and Nicolas: That's true. It gives the headers not the file names. ...
written 11 months ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... Hi Pierre! Thanks for the fast reply. This command, however, would give me the 10 fasta files that have the highest number of redundant headers within the same file. There are no redundant headers in each of my files. What I need is to find the 10 fasta files with the highest number of identical/red ...
written 11 months ago by jan0
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Finding fasta files that share the highest number of identical headers
... Hello, I have about 100 fasta files and need to find those 10 that share the highest number of identical headers. I.e., I am looking for the 10 fasta files for which the number of species that are present in all of them is the highest. Any idea how to do that? A script (perl, python, bash) would be ...
perl python sequence script fasta written 11 months ago by jan0 • updated 11 months ago by 5heikki7.8k
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Comment: C: Merging of sequence chunks
... Thanks JC, the script is doing the job! ...
written 11 months ago by jan0

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Popular Question 5 months ago, created a question with more than 1,000 views. For How to remove sequences from a fasta file based on ID list?

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