YanWangTF
@WangLab-UToronto PI working on fungus-insect symbiosis, fungal genome evolution, and comparative genomics.
University of TorontoToronto, Canada
Pinned Repositories
Calcu_Identity
reads a .delta.filter.coords output and calculate the percentage of identity among the matches
CodonTrim
reads a codon alignment (fasta from the 1st pos)--trim the remaining ends if not end with 3.
Filter_len
filter out short multiple sequence alignment file for phylogenomic analyses
HGTfilter
Filter out the potential horizontal gene transferred element based on a similarity comparison method
Ortho_Rep
Isolate ortholog-representatives from each individual according to an MCL-based method
PlotMidPointRootTree
Find_mutual_BestHit
Identify reciprocal best BLASTp hits
AGF_phylogenetics
Alignment files used in the Wang_et_al_2018_AGF_manuscript
Alignment_Knudsen_et_al_2020
This repository includes the alignment file used to reconstruct the phylogenetic tree (in both .nex and .phy formats) as well as the partition file and a prefix file containing the taxa name information.
Alignment_Knudsen_et_al_2024
YanWangTF's Repositories
YanWangTF/Smittium_minutisporum_GenomeAnnotation
YanWangTF/Alignment_Knudsen_et_al_2024
YanWangTF/ML
YanWangTF/Wang_et_al_2023_aln_files
YanWangTF/HGTfilter
Filter out the potential horizontal gene transferred element based on a similarity comparison method
YanWangTF/Strongman-Wang_2022_aln-phylo
YanWangTF/Paraglomus_fungi_odb10_aln
YanWangTF/Alignment_Knudsen_et_al_2020
This repository includes the alignment file used to reconstruct the phylogenetic tree (in both .nex and .phy formats) as well as the partition file and a prefix file containing the taxa name information.
YanWangTF/phylum_retriever
YanWangTF/AGF_phylogenetics
Alignment files used in the Wang_et_al_2018_AGF_manuscript
YanWangTF/PlotRidgeMap.R
This R script is used to plot ridge map of each domain for a given table (column names are domains)
YanWangTF/PlotMidPointRootTree
YanWangTF/CodonTrim
reads a codon alignment (fasta from the 1st pos)--trim the remaining ends if not end with 3.
YanWangTF/Filter_len
filter out short multiple sequence alignment file for phylogenomic analyses
YanWangTF/Calcu_Identity
reads a .delta.filter.coords output and calculate the percentage of identity among the matches
YanWangTF/Find_mutual_BestHit
Identify reciprocal best BLASTp hits
YanWangTF/Ortho_Rep
Isolate ortholog-representatives from each individual according to an MCL-based method