evolbeginner
Sishuo Wang, Dept Microbiol, faculty of Med, CUHK. Dabbling in phylogenetics, microbial evolution and genomics.
CUHKHong Kong
Pinned Repositories
angst
A wrapper of AnGST (https://github.com/almlab/angst)
basic_process_mini
basic_process_mini
bs_inBV
A tool to help generate the file in.BV when using "complex" substitution models for MCMCtree. Particularly, the hessian is approximated by a bootstrap approach.
correlTraitGene
generateAlnFromOrthoFinder
iSeeCE
A pipeline for identifying concerted evolution between duplicates based on gene position and phylogenetic evidence. See "Publications" below for the background.
modeltest_phylo
A pipeline combining modeltest (jmodeltest, prottest), phylogenetic reconstruction (phyml, raxml), topology comparison (CONSEL)
ortho2cdd
from orthofinder to cdd annotation
rrtc
a script to do probability-based relaxed time constraint-based dating
Solutions_Manual_CME2006_MESA2014
A solutions manual for all excercises in the Ziheng Yang's two seminal books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).
evolbeginner's Repositories
evolbeginner/modeltest_phylo
A pipeline combining modeltest (jmodeltest, prottest), phylogenetic reconstruction (phyml, raxml), topology comparison (CONSEL)
evolbeginner/bs_inBV
A tool to help generate the file in.BV when using "complex" substitution models for MCMCtree. Particularly, the hessian is approximated by a bootstrap approach.
evolbeginner/iSeeCE
A pipeline for identifying concerted evolution between duplicates based on gene position and phylogenetic evidence. See "Publications" below for the background.
evolbeginner/rrtc
a script to do probability-based relaxed time constraint-based dating
evolbeginner/correlTraitGene
evolbeginner/generateAlnFromOrthoFinder
evolbeginner/ortho2cdd
from orthofinder to cdd annotation
evolbeginner/angst
A wrapper of AnGST (https://github.com/almlab/angst)
evolbeginner/basic_process_mini
basic_process_mini
evolbeginner/basic_sequence_processing_mini
mini scripts for sequence processing
evolbeginner/Solutions_Manual_CME2006_MESA2014
A solutions manual for all excercises in the Ziheng Yang's two seminal books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).
evolbeginner/bioruby
bioruby
evolbeginner/brady
some scripts for brady project
evolbeginner/Bradyrhizobium-Nif-HGT
evolbeginner/dating
custom scripts for molecular clock analysis, mainly mcmctree
evolbeginner/graphics
scripts used to do graphic work
evolbeginner/hahaha
evolbeginner/HGT
HGT Rhizobiales
evolbeginner/Jan_SL
evolbeginner/mcmctree
evolbeginner/multistate
for BayesTraits multistate analysis
evolbeginner/packages
evolbeginner/phylo_mini
mini scripts for phylogenetic analyses related stuff
evolbeginner/pymc
Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Aesara
evolbeginner/Roseobacter_pseudogene
evolbeginner/scm
stochastic character mapping and asr
evolbeginner/searchBlast
evolbeginner/SEQ2TREE
evolbeginner/stat
simple scripts for statistics
evolbeginner/taxa_search