evolbeginner
Sishuo Wang, Dept Microbiol, CUHK. Dabbling in phylogenetics, microbial evolution and genomics. If not otherwise specified, all scripts under GPL-3.0.
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/basic_sequence_processing_mini
mini scripts for sequence processing
evolbeginner/others
scripts for other uses
evolbeginner/triple_asymmetric_evol
evolbeginner/search_4_dupli_and_single
To search for duplicates and singletons based on BLAST results
evolbeginner/gff2fasta
evolbeginner/WAGC
evolbeginner/run_orthomcl
script to do Orthomcl
evolbeginner/PLT
evolbeginner/tba_wrapper
evolbeginner/tba
evolbeginner/PAML
evolbeginner/linc_dupli_associated
evolbeginner/EntrezEfetch
evolbeginner/DNA_methyl_parsing
evolbeginner/RPP
RNA-seq data processing pipeline
evolbeginner/linc
evolbeginner/NGS_basic_processing_mini_tools
evolbeginner/bioruby-taxa
TODO: one-line summary of your gem
evolbeginner/i-adhore3_helper
evolbeginner/domain_drawing
evolbeginner/intermine
A powerful open source data warehouse system
evolbeginner/gene_conversion_in_mtr
evolbeginner/dimer_project
evolbeginner/microRNA_duplication_project
evolbeginner/protein_sec_struc_predict
evolbeginner/specialized_tools
evolbeginner/process_from_NCBI_fasta