- Dr Weizhi Song
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong
- E-mail: songwz03@gmail.com
-
TreeSAK has been tested on Linux/Mac, but NOT yet on Windows.
-
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 v1.28.0 :::...
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
ConvertMSA -> Convert MSA format
fa2phy -> Convert MSA format (fasta to phylip)
SingleLinePhy -> Put sequences in single line in phylip format
OneLineAln -> One-line fasta format alignments
SliceMSA -> Slice MSA by column
AlignmentPruner -> Remove heterogenous sites from MSA
BMGE -> Run BMGE
ConcateMSA -> Concatenate MSA
Tree-related
MarkerSeq2Tree -> Marker sequence to tree
MarkerRef2Tree -> Marker (reference sequence) to Tree
GTDB_tree -> get GTDB tree
PMSF -> run iqtree with PMSF
subset_tree -> 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
ALE -> Modules for running ALE
GeneRax -> Run GeneRax (to be added)
RootTree -> Root tree with outgroup leaves
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