- Dr. Weizhi Song
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong
- E-mail: songwz03@gmail.com
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TreeSAK has been tested on Linux/Mac, but NOT yet on Windows.
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TreeSAK is implemented in python3, you can install it with pip3:
# for the first time installation pip3 install TreeSAK # for updating pip3 install --upgrade TreeSAK
...::: TreeSAK v1.38.7 :::...
Marker-related
ExtractMarkerSeq -> Extract marker by blastn
parse_deltall_stdout -> Parse stdout of deltaLL.rb
get_arCOG_seq -> Retrieve arCOG sequences
AssessMarkerPA -> Assess Markers by P/A among groups
SplitScore -> Assess markers by split score
AssessMarkerDeltaLL -> Assess Markers by DeltaLL
OMA -> Prepare input files for running OMA
OMA2 -> Filter OMA predicted OGs
Multiple Sequence Alignment
BMGE -> Run BMGE
pruneMSA -> Prune MSA with alignment_pruner.pl
recodeAA -> Recode amino acids to Dayoff 4, Dayoff 6 or SR4 categories
fa2phy -> Convert MSA format (fasta to phylip)
SliceMSA -> Slice MSA by column
ConcateMSA -> Concatenate MSA
ConvertMSA -> Convert MSA format
OneLineAln -> One-line fasta format alignments
SingleLinePhy -> Put sequences in single line in phylip format
CS_trim -> (to be added) perform chi-squared trimming to reduce compositional heterogeneity
gap_stats -> The percentage of gap in each sequence of a MSA
Tree-related
iTOL -> Prepare iTOL files
PB -> Infer tree with PhyloBayes-MPI
AssessPB -> Compare PhyloBayes chains
MarkerSeq2Tree -> Marker sequence to tree
MarkerRef2Tree -> Marker (reference sequence) to Tree
GTDB_tree -> get GTDB tree
subset -> Subset tree
compare_trees -> Compare trees with Mantel test
rename_leaves -> Rename tree leaves
print_leaves -> print out tree leaves
FLN -> Format leaf names (e.g. remove spaces in names)
ModifyTopo -> Modify tree topology
GeneRax -> (to be added) Run GeneRax
ALE -> Modules for running ALE
RootTree -> Root tree with outgroup leaves
RootTreeGTDB214 -> Root tree by GTDB taxonomy (r214)
RootTreeGTDB220 -> Root tree by GTDB taxonomy (r220)
LcaToLeaves -> Get two leaves that define an internal node
replace_clade -> Replace tree clade
Model-related
PMSF -> run iqtree with PMSF
PPA -> (to be added) Perform Posterior Predictive Analysis (across-site)
Dating-related
Dating -> Perform molecular dating
AssessCVG -> Assess dating convergence
CompareMCMC -> Compare MCMCTree outputs
PlotMcmcNode -> distribution of node's age estimation
VisHPD95 -> HPD95 of estimated node age
pRTC -> Perform probabilistic RTC dating
Phylo-related stats
PhyloBiAssoc -> A wrapper for binaryPGLMM test