Modeling gene duplication, loss, and coalescence
License
Unknown, GPL-2.0 licenses found
Licenses found
Unknown
LICENSE
GPL-2.0
COPYING
mdrasmus/dlcoal
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
master
Could not load branches
Nothing to show
Could not load tags
Nothing to show
{{ refName }}
default
Name already in use
A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code
-
Clone
Use Git or checkout with SVN using the web URL.
Work fast with our official CLI. Learn more.
- Open with GitHub Desktop
- Download ZIP
Sign In Required
Please sign in to use Codespaces.
Launching GitHub Desktop
If nothing happens, download GitHub Desktop and try again.
Launching GitHub Desktop
If nothing happens, download GitHub Desktop and try again.
Launching Xcode
If nothing happens, download Xcode and try again.
Launching Visual Studio Code
Your codespace will open once ready.
There was a problem preparing your codespace, please try again.
Latest commit
Git stats
Files
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
DLCoal (duplications, losses, and coalescence) http://compbio.mit.edu/dlcoal/ Matthew Rasmussen ============================================================================= ABOUT DLCoal is a software package containing the DLCoalRecon program as well as several other useful utilities for working with gene trees. DLCoalRecon is a reconciliation program that maps a gene tree to species tree in order to determine how gene duplications and losses have occurred. DLCoalRecon's unique feature is that it can perform reconciliation despite the presence of incomplete linegae sorting. DLCoal citation: Rasmussen, Kellis. A unified model of gene duplication, loss, and coalescence using a locus tree. Genome Research. 2012. ============================================================================= DEPENDENCIES DLCoal has the following requirements: - GNU Scientific library (GSL) http://www.gnu.org/software/gsl/ - Python (2.5 or greater) http://python.org/ ============================================================================= INSTALL NOTE: Makefile installation will work best on UNIX or CYGWIN (Windows). To compile the DLCoal library use the Makefile. make Once compiled, to install the DLCoal programs (default install in /usr) use: make install To specify your own installation path use: make install prefix=/usr/local DLCoal can also run directly from the source directory. Simply add the bin/ directory to your PATH or create symlinks to the scripts within bin/ to any directory on your PATH. ============================================================================= USAGE Running dlcoal_recon with no arguments will print out its command-line usage: Usage: dlcoal_recon [options] GENE_TREE1 [GENE_TREE2 ...] Options: -h, --help show this help message and exit -s SPECIES_TREE, --stree=SPECIES_TREE species tree file in newick format (myr) -S GENE_TO_SPECIES_MAP, --smap=GENE_TO_SPECIES_MAP gene to species map -n POPULATION_SIZE, --popsize=POPULATION_SIZE Effective population size -D DUPLICATION_RATE, --duprate=DUPLICATION_RATE rate of a gene duplication (dups/gene/myr) -L LOSS_RATE, --lossrate=LOSS_RATE rate of gene loss (losses/gene/myr) -g GENRATION_TIME, --gentime=GENRATION_TIME generation time (years) -i ITERATIONS, --iter=ITERATIONS number of search iterations File extensions: -I INPUT_EXT, --inext=INPUT_EXT input file extension (default='') -O OUTPUT_EXT, --outext=OUTPUT_EXT output file extension (default='.dlcoal') Miscellaneous: --nprescreen=NUM_PRESCREENS number of prescreening iterations --nsamples=NUM_SAMPLES number of samples for dup-loss integration (default=100) --init-locus-tree=TREE_FILE initial locus tree for search -x RANDOM_SEED, --seed=RANDOM_SEED random number seed -l, --log if given, output debugging log #============================================================================= # Examples See examples/make.sh for an example of how to use each program in the DLCoal package. #============================================================================= # Documentation See doc/dlcoal-manual.html for further documentation of the software and its associated file-formats.
About
Modeling gene duplication, loss, and coalescence
Resources
License
Unknown, GPL-2.0 licenses found
Licenses found
Unknown
LICENSE
GPL-2.0
COPYING
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published