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smirarab
PASTA (Practical Alignment using SATe and Transitivity)
Hello, just installed pasta and was trying to check it out, however I ran into this error the first time I ran it (initially was in my Dropbox folder and...
currently the distinction between insertion and normal lines are lost when going from initial alignment to PASTA code.
Dendropy with version higher than 4.5.2 breaks compatibility. One example is `_convert_node_to_root_polytomy` which was a function and became a method of the `Node` class.
Hi, I run into this problem when running "run_pasta.py --input=filtered.faa --datatype=Protein": PASTA failed because one of the programs it tried to run failed. The invocation that failed was: ".../.conda/envs/pasta/bin/hmmeralign" ".../.conda/envs/pastajob/tempsgmw9sal/init_aln/temphmmeraligntkj6o3kq/input.fasta"...
Tree parse error: unexpected token '_os_78_oe_ropschr02g03077' -- not recognized as a sequence name
Hi, **I'm running PASTA thus:** `run_pasta.py --aligner=mafft --merger=muscle --tree-estimator=fasttree --num-cpus=4 --datatype=protein -i pep/og00090.pep -o 1pasta/og00090` **and getting this erro:** PASTA failed because one of the programs it tried to run...
Hi, I have a trouble when I'm running test `run_pasta.py -i small.fasta` /usr/local/bin/run_pasta.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').require('PASTA==1.9.1') PASTA INFO: Reading input sequences from 'small.fasta'......
Hello! I'm working with a program called ROADIES ([link)](https://github.com/TurakhiaLab/ROADIES) that uses PASTA. ROADIES basically produces guide trees from provided genome assemblies by selecting a bunch of random "c-genes" (non-recombining sites...
