sepp
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smirarab
Ensemble of HMM methods (SEPP, TIPP, UPP)
Hi, I get this error when trying to use UPP: "PASTA ERROR: PASTA is exiting because of an error: '/rds/general/user/userid/home/anaconda3/lib/python2.7/site-packages/PASTA-1.7.8-py2.7.egg/bin/mafft' not found. Please install 'mafft' and/or configure its location correctly...
Hi @smirarab, can you please have a look at an issue in our [qiime2 forum](https://forum.qiime2.org/t/non-16s-seqs-inserted-into-gg13-8-ref-tree-by-sepp/10561). A user found a situation in which SEPP inserts fragments even though they are only...
It would be great if you could add Selenocysteine ("U") to the set of acceptable amino acids.
Current alignment size set to 10%, needs to be set to 10.
MAC file directory is case insensitive so TIPP's reference directory does not work correctly for it because of the pyrG and pyrg folders. Change the name and make them not...
Hi Siavash, First, the SEPP, TIPP, UPP and HIPPI suite look very interesting and I'm excited to try them out - SEPP in particular I'm wondering if it would it...
We can output the number of fragmentary sequences to INFO. We can also output their names (maybe to LOG?)
chdir to this directory /scratch/cluster/namphuon/metagen/test2 Run this command to reproduce it: /lusr/bin/python run_tipp.py -t /projects/sate5/metagen/data/refpkg/rpsB.refpkg/sate.taxonomy -a /projects/sate5/metagen/data/refpkg/rpsB.refpkg/sate.fasta -r /projects/sate5/metagen/data/refpkg/rpsB.refpkg/sate.taxonomy.RAxML_info -x 1 -at 0.95 -pt 0.95 -tx /scratch/cluster/namphuon/metagen/refpkg/rpsB.refpkg/all_taxon.taxonomy -txm /scratch/cluster/namphuon/metagen/refpkg/rpsB.refpkg/species.mapping -adt...
In SEPP, alignment might not be of any interest. Creating a merged alignment can take unnecessary time. That output should be made optional.
Breaking edges in the placement decomposition creates weird situations where something is on an edge that doesn't even exists in the actual tree. We should change this such that placement...