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mmprofiler's Issues

mmprofiler not on conda

@SilasK wasn't this working before- was it removed from conda? Thanks!

e.g.

$ conda install mmprofiler
Collecting package metadata: done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - mmprofiler

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Profile parameters

mmseqs msa2profile --help

prefilter options default description [value range]
--comp-bias-corr	1 correct for locally biased amino acid composition [0,1]

align options default description [value range]
--gap-open 11 Gap open cost
--gap-extend 1 Gap extension cost

profile options default description [value range]
--match-mode 0 0: Columns that have a residue in the first sequence are kept, 1: columns that have a residue in --match-ratio of all sequences are kept.
--match-ratio 0.500 columns that have a residue in this ratio of all sequences are kept
--pca 0.000 pseudo count admixture strength
--pcb 1.500 pseudo counts: Neff at half of maximum admixture (0.0,infinity)
--wg false use global sequence weighting for profile calculation
--filter-msa 1 filter msa: 0: do not filter, 1: filter
--cov 0.000 filter output MSAs using min. fraction of query residues covered by matched sequences [0.0,1.0]
--qid 0.000 reduce diversity of output MSAs using min.seq. identity with query sequences [0.0,1.0]
--qsc -20.000 reduce diversity of output MSAs using min. score per aligned residue with query sequences [-50.0,100.0]
--max-seq-id 0.900 reduce redundancy of output MSA using max. pairwise sequence identity [0.0,1.0]
--diff 1000 filter MSAs by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50


@berkelem @chris-rands FYI

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