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CHANGES.txt
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################
# POTION-1.1.2 #
################
Commit date: 09/24/2015
- Bug fixes;
- POTION could get stuck when using AlignIO BioPerl module to change alignment
files from phylip to fasta and vice-versa (now POTION does not rely on BioPerl
to perform this step)
################
# POTION-1.1.1 #
################
Commit date: 09/18/2015
- Bug fixes;
- POTION could not find output files produced by prank (prank changed its
output file name since the version we used to validate POTION)
- POTION was stuck when parsing trimAl output file containing sequence
identity metrics
- POTION could not print proper information about some excluded groups/genes
- Now it is much easier to create POTION configuration files!
- When executing POTION to create a new configuration file (--create_conf
parameter) it is possible to use several other parameters to tell POTION how
it should fills in the appropriate information. For more information about
this new feature please execute POTION with --help parameter or read
README.txt file. Please notice that old configuration files will probably not
work with this new version of POTION.
- POTION now supports additional parameters to filter sequences and groups
based on identity metrics.
- These metrics are intended to complement the existing ones, and may be
especially useful to remove groups likely to take a long time to compute
(refer to our article for a more detailed discussion about these groups). In
brief, groups with an elevated mean sequence identity (close to 100%) that
usually contain only a few distinct kinds of sequences are likely to get
stuck. For those groups it appears that the likelihood functions of codeml
and phyml/phylip do not converge quickly to a maximum. Specifically, these
new variables now are available for users to further configure POTION
behavior and remove sequence and groups based on maximum identity values. For
groups, for instance, it could be useful to set max_group_identity to values
around 99% to remove groups where there is no sufficient diversity to detect
positive selection but are likely to get stuck during codeml execution. The
new variables implemented are:
- max_sequence_identity: maximum (mean/median) sequence identity cutoff
- sequence_identity_average_metric: which metric should be used when
computing sequence identity metric (mean/median)
- sequence_identity_comparison: which kind of sequence should be used when
comparing sequences (nt/aa)
- max_group_identity: maximum mean group identity cutoff
- group_identity_comparison: which kind of sequence should be used when
comparing groups (nt/aa)
##############
# POTION-1.1 #
##############
Commit date: (08-05-2015)
- Bug fixes;
- POTION now supports PhyML for phylogenetic tree reconstruction (beta, not
extensively tested). To use it first configure POTION so it knows where
to find PhyML (path for phyml is located at "config_files/potion_config")
and set POTION to use it for phylogenetic tree reconstruction (set
"phylogenetic_tree" parameter (found in POTION's configuration file)
to either phyml_nt or phyml_aa to use nucleotide or amino acid sequences,
respectivelly.