matOptimize
matOptimize is a program used to optimize phylogenies using parsimony score. It is used on MAT files, which can be created by UShER.
Installation
To install matOptimize, simply follow the directions for installing UShER, and matOptimize will be included in your installation.
Options
-v [ --vcf ] arg Input VCF file (in uncompressed or
gzip-compressed .gz format)
-t [ --tree ] arg Input tree file
-T [ --threads ] arg (=12) Number of threads to use when possible
[DEFAULT uses all available cores, 12
detected on this machine]
-i [ --load-mutation-annotated-tree ] arg
Load mutation-annotated tree object
-o [ --save-mutation-annotated-tree ] arg
Save output mutation-annotated tree
object to the specified filename
[REQUIRED]
-r [ --radius ] arg (=-1) Radius in which to restrict the SPR
moves.
-S [ --profitable-src-log ] arg (=/dev/null)
The file to log from which node a
profitable move can be found.
-a [ --ambi-protobuf ] arg Continue from intermediate protobuf
-s [ --minutes-between-save ] arg (=0)
Minutes between saving intermediate
protobuf
-m [ --min-improvement ] arg (=0.000500000024)
Minimum improvement in the parsimony
score as a fraction of the previous
score in ordder to perform another
iteration.
-d [ --drift_iteration ] arg (=0) Iterations permiting equally
parsimonious moves after parsimony
score no longer improves
-n [ --do-not-write-intermediate-files ]
Do not write intermediate files.
-N [ --max-iterations ] arg (=1000) Maximum number of optimization
iterations to perform.
-M [ --max-hours ] arg (=0) Maximium number of hours to run
-V [ --transposed-vcf-path ] arg Auxiliary transposed VCF for ambiguous
bases, used in combination with usher
protobuf (-i)
--version Print version number
-z [ --node_proportion ] arg (=2) the proportion of nodes to search
-y [ --node_sel ] arg Random seed for selecting nodes to
search
-h [ --help ] Print help messages
Presentations
Cheng Ye has presented matOptimize at The Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), held virtually on July 25-30, 2021. You can find his slides here.