Pinned Repositories
AdmixTools
Tools test whether admixture occurred and more
alan
Alignment viewer for linux terminal
Anacapa
#### Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
AntCaller
SNP calling and genotyping for damaged DNA
ASTRAL
Accurate Species TRee ALgorithm
Augustus
Genome annotation with AUGUSTUS
bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
beagle-lib
general purpose library for evaluating the likelihood of sequence evolution on trees
Chrom-Compare
Population_Genomics_Scripts
Scripts of population genomics analysis
mcassatt's Repositories
mcassatt/Population_Genomics_Scripts
Scripts of population genomics analysis
mcassatt/AdmixTools
Tools test whether admixture occurred and more
mcassatt/alan
Alignment viewer for linux terminal
mcassatt/Anacapa
#### Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
mcassatt/AntCaller
SNP calling and genotyping for damaged DNA
mcassatt/ASTRAL
Accurate Species TRee ALgorithm
mcassatt/Augustus
Genome annotation with AUGUSTUS
mcassatt/bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
mcassatt/beagle-lib
general purpose library for evaluating the likelihood of sequence evolution on trees
mcassatt/Chrom-Compare
mcassatt/gatk
Official code repository for GATK versions 4 and up
mcassatt/gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
mcassatt/grenepipe
Snakemake pipeline for variant calling from raw sequences
mcassatt/mapping-iterative-assembler
Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria
mcassatt/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
mcassatt/mtAnnotate
Java program to transfer DNA annotations from a GenBank file to a FASTA sequence, intended for closely related mitochondrial genomes.
mcassatt/ngsLD
Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
mcassatt/North-American-Ice-Sheets
History of ice sheets and ice caps from the Last Glacial Maximum to present in North America, as produced by Dyke et al. (2003) and Dyke (2004)
mcassatt/paper-zhang2014
Source code from Zhang et al., (2014) Genomic data of avian phylogenomics project. GigaScience 3:26
mcassatt/partitionfinder
PartitionFinder discovers optimal partitioning schemes for DNA sequences.
mcassatt/popgen-notes
Population genetics notes
mcassatt/pophistory-tutorial
Tutorial on using popular tools for learning about population history
mcassatt/pyule
CLI tool for simple calculations of rates and tree heights and lengths under Yule processes.
mcassatt/raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
mcassatt/Sea-Cow
This repository includes the pipeline and commands which will useful for the paleogenome analysis
mcassatt/SeqPrep2
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
mcassatt/simpred
SNV impact predictor
mcassatt/SnpEff
mcassatt/standard-RAxML
mcassatt/tracer
Posterior summarisation in Bayesian phylogenetics