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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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checkM tree_qa newick trees in wrong format #134

Closed celiosantosjr closed 6 years ago

celiosantosjr commented 6 years ago

I am running checkM tree and tree_qa to obtain an idea of the taxa insertion high of my bins. But, when I run the commands all works and generate files that I cannot use in any tree rendering software. They all say the format is wrong. Reading in the internet, I discovered that the format really is wrong but the changes suggested by them:

perl -pe "s/;/+/g" tree_tax.nwk | perl -pe "s/+\n/;\n/g" > tree_tax.fixed.nwk

Still does not work, since the taxa names do not appear in the final tree. Thank you in advance.

donovan-h-parks commented 6 years ago

What specifically is wrong with the current format? I view the trees in Dendroscope.

donovan-h-parks commented 6 years ago

Closed due to inactivity.