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GDKO / AvP

Automatic evaluation of HGTs
GNU General Public License v3.0
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how to infer donor species according to result file named fasttree_tree_results.txt_k5.prox.txt #12

Closed njliangdong closed 5 months ago

njliangdong commented 8 months ago

Hi, dear author, I used AvP to perform genome-wide HGT events identification, and it work well. However, my next focus is how can I summarize the donor species of HGT candidates, from fastree output (phylogeny tree or anything else)?

Thanksa lot !

GDKO commented 7 months ago

Hi @njliangdong,

Have you run classify?

Cheers, Georgios

njliangdong commented 7 months ago

Hi @njliangdong,

Have you run classify?

Cheers, Georgios

Hi @njliangdong,

Have you run classify?

Cheers, Georgios

yes, I do and one folder named Avp.classify was generated, which include one file named 'classification_results.txt', I am not sure if this file provide the donor info of HGTs, thanks for your further reply !

GDKO commented 7 months ago

The classify command groups donors based on the classification file but with a broad taxonomic ranking (see taxonomy file). Are you more interested in lower ranks?