ammodramus
Computational biologist, population geneticist. Ammodramus, from ammos (άμμος) "sand", drameas (δρομέας) "runner", genus of American grassland sparrows.
Pinned Repositories
alnclst
A simple UCLUST-like clustering algorithm for pre-aligned sequences with built in recentering
ammodramus.github.io
angsd
Program for analysing NGS data.
coalseam
Simulating coalescence through population pedigrees
discoal
(fork with minor changes to output) discoal is a coalescent simulation program capable of simulating model with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples. This is a minor fork that changes the output slightly.
ebsom
Empirical Bayes somatic variant calling
mope
Infer the dynamics of mitochondrial heteroplasmy during different life stages using population genetics and phylogenetics
opl
Analysis scripts and notebooks accompanying a paper on mitochondrial heteroplasmy in humans
R-labs
Introduction to (base) R for biologists
tsmc
triploid SMC inference method
ammodramus's Repositories
ammodramus/mope
Infer the dynamics of mitochondrial heteroplasmy during different life stages using population genetics and phylogenetics
ammodramus/coalseam
Simulating coalescence through population pedigrees
ammodramus/discoal
(fork with minor changes to output) discoal is a coalescent simulation program capable of simulating model with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples. This is a minor fork that changes the output slightly.
ammodramus/tsmc
triploid SMC inference method
ammodramus/alnclst
A simple UCLUST-like clustering algorithm for pre-aligned sequences with built in recentering
ammodramus/ammodramus.github.io
ammodramus/angsd
Program for analysing NGS data.
ammodramus/ebsom
Empirical Bayes somatic variant calling
ammodramus/opl
Analysis scripts and notebooks accompanying a paper on mitochondrial heteroplasmy in humans
ammodramus/R-labs
Introduction to (base) R for biologists
ammodramus/demographic_lstm
ammodramus/hair
analysis of mtDNA heteroplasmy in hair samples
ammodramus/infsites
A program to calculate exact sampling probabilities under the infinite sites mutation model in one or two demes
ammodramus/jupyter-vim-binding
Jupyter meets Vim. Vimmer will fall in love.
ammodramus/microplink
Fast and minimal PLINK file processing with numba
ammodramus/NCBI_taxonomy_tree
NCBI taxonomy tree in-memory mapping
ammodramus/psmc
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
ammodramus/pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
ammodramus/wrightfishersim