-
Notifications
You must be signed in to change notification settings - Fork 7
License
balabanmetin/uDance
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
uDance version 1.6.3 AUTHORS: Metin Balaban Yueyu Jiang Prerequisites: Unix/Linux Anaconda raxml-ng (if desired) Usage: snakemake -c 4 --configfile config.yaml --snakefile udance.smk all In the config.yaml, specify `workdir`. Multiple sequence alignments should be located under `workdir`/alignments. If there is a backbone tree as well, locate it as `workdir`/backbone.nwk and set backbone: "tree" in config.yaml Changelog: 1.6.3 -Cluster size can be automatically set -Bug fix 1.6.2 -Backbone filtering can be turned on or off 1.6.1 -Benchmarks directives are used in udance.smk 1.6.0 -Skip a partition (return backbone) if the number of placements is it less than a desired number -Bug fixes 1.5.1: -Output tree may have branch lengths in substitution unit if desired. 1.5.0: -uDance uses ASTRAL version 5.17.2, which supports both multithreading and constrained search. 1.4.1: -Performance improvements in placement_prep -Keep placement_prep intermediate files. Changelog: 1.4.0: -Stitching algorithm outputs a new tree named maxqs which picks the best one of the two ASTRAL trees for each partition. 1.3.3: -Default decompose edge threshold changed -Bug fixes -Large cluster pruning strategy is changed to serial search (instead of binary) 1.3.2: -Expose backbone selection strategy to the user -Expose gene tree filtering parameters at refine stage to the user 1.3.1: -Getting rid of pruning thresholds (automated finding) 1.3.0: -Pruning Large partitions -Changes in TreeCluster logic disallowing formation of very small partitions 1.2.1: -APPLES2 excludes sequences that are placed on internal nodes. -Filtered backbone sequences are no longer added to the query set. Tips/Tricks: -Set min_placements: 9999999 to only filter out low quality backbone sequences and return. -Set config["mainlines_config"]["n"] to number of species in the dataset and config["backbone"] to "de-novo". Then run snakemake with target {outdir}/backbone.nwk. This will do species tree inference without divide and conquer.
About
No description, website, or topics provided.
Resources
License
Stars
Watchers
Forks
Packages 0
No packages published