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roblanf / sarscov2phylo

Global phylogenies of SARS-CoV-2 sequences
GNU General Public License v3.0
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Codes are missing #23

Closed hforoughmand closed 1 year ago

hforoughmand commented 1 year ago

The new approach is to keep the tree and update it via for example scripts/add_seqs_to_tree.sh. But the bash script file doesn't contain the code. Is that a problem with the codes or with the github repository? Also there is a scripts/add_seqs_to_global_tree.sh which is also only some lines of comments. Please help me in getting the updated codes.

roblanf commented 1 year ago

Hi @hforoughmand, please don't use this repo to build trees of SARS-CoV-2 any more.

I suggest instead using UShER and matOptimize, which you can find here: https://usher-wiki.readthedocs.io/en/latest/matOptimize.html

roblanf commented 1 year ago

I updated the readme to make this clear!

I also put a link to MAPLE in the readme. Please check that out too - it's another tool built spefically for estimating big trees of SARS-CoV-2.