Entering edit mode
2.3 years ago
omaridris5315
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10
How do you remove extra information being added to fasta alignments? I have the tree already in newick or nexus I need to do some regex using python. Is newick tricky to iterate with file open as? Is there built in staff? The extra information is either underlined or spaced. The second problem is if I want to add taxonomic name to the taxon id how would I do that? Do I have to use entrez pick my id for each sequence then paste it and then search I have not used entrenze yet but I see you can use id from gene bank file. But then I do not know what object or name you use to get taxonomic names. This will take forever as ncbi may not allow one by one request. I do not have specific group my sequences come from different frog species. Thanks
Archaeopteryx is a good tree editor, which includes functions to retrieve taxonomic information from a Newick or Nexus tree, if the names are NCBI accession numbers.
To get an idea of what you can do with Archaeopteryx, see the tutorial Visualization of Phylogenetic Trees.
No. I have used Arch before. I can edit manual also in Mega or iTOL. iTOL has auto labeling of the id on a tree. It used to be available for free on iTOL. Not anymore. I do not know if it is available for subscription. I have close to 200 taxa. I have four types of tree analysis Bates beast Zia and RAXML. To compare them easily I need complete label:id+scientific name. RAXML can allow upto250 characters long labels so it works. However, I have a little problem that the alignment software Maffts adds some numbers I think they are start and end sequence numbers after the id(taxon) which makes it look ugly and I do not want to remove it by hand. I guess I have no option. I have some programming skills. But it may take time before I develop it to do it manually and label each tree tip by first removing each extra number from newick tree then connecting to ncbi data base or blast search each id retrieve the corresponding species name then append it to newer tree. I need to publish it soon and I do not need to waste time on this right now. Otherwise I will just go manual for now until I work it out in the future.
oh my bad I see it automatically adds labels