Cleaning up with sed 2
Posted: 2017-07-08 Filed under: academic | Tags: clean, fasta, grep, sed, sequence Leave a commentI have a list of nucleotide sequences in fasta format, obtained from NCBI. I want to clean the sequences names, leaving only the accession numbers. Additionally, I want to extract the accession numbers to a separate list. I am not that familiar with sed, since I use it mainly in my SlackBuilds to fix small things. Therefore, for my fuuture reference, I decided to sum things up.
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Cleaning up with sed
Posted: 2017-03-31 Filed under: academic | Tags: clean, phylogenetic tree, phylogeny, SeaView, sed, TimeTree, txt Leave a commentI needed to clean up some plain text files from data and characters I did not want.
To be more precise, I have a phylogenetic tree, obtained from the TimeTree web-site. Species presented there are mainly birds, several reptiles and a fish. The tree has branches length information and node labels, which I wanted to remove.
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