- 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 v1.58.0 :::...
Marker-related
ExtractMarkerSeq -> Extract marker by blastn
deltall -> 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
filter_rename_ar53 -> Filter rename GTDB markers
Multiple Sequence Alignment
BMGE -> Run BMGE
pruneMSA -> Prune MSA with alignment_pruner.pl
recode -> Recode amino acids to Dayoff 4, Dayoff 6 or SR4 categories
fa2phy -> Convert MSA format (fasta to phylip)
phy2fa -> Convert MSA format (phylip to fasta)
SliceMSA -> Slice MSA by column
ConcateMSA -> Concatenate MSAs
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
batch_itol -> Batch access iTOL
iTOL_gene_tree -> Genome metadata to gene metadata
iTOL_msa_stats -> iTOL_msa_stats
PB -> Infer tree with PhyloBayes-MPI
assessPB -> Compare PhyloBayes chains
supertree -> Infer species tree from multiple gene trees
MarkerSeq2Tree -> Marker sequence to tree
MarkerRef2Tree -> Marker (reference sequence) to Tree
GTDB_tree -> Get GTDB tree
subset -> Subset tree
TaxonTree -> Subset GTDB tree by taxon
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
cogTree -> Infer tree for individual COG function
koTree -> Infer tree for individual KEGG function
RootTree -> Root tree with outgroup leaves
RootTreeGTDB -> Root tree by GTDB taxonomy
LcaToLeaves -> Get two leaves that define an internal node
replace_clade -> Replace tree clade
GeneTree -> Infer gene tree
guide_tree -> Prepare guide tree for iqtree
get_lca_id -> Get LCA id
tree_fmt -> Change tree format
rm_leaf -> Remove leaf/leaves from tree
Model-related
PMSF -> run iqtree with PMSF
PPA -> (to be added) Perform Posterior Predictive Analysis (across-site)
Dating-related
dating -> Perform molecular dating
CompareMCMC -> Compare MCMCTree outputs
PlotMcmcNode -> Distribution of node's age estimation
VisHPD95 -> HPD95 of estimated node age
pRTC -> Perform probabilistic RTC dating
mcmcTC -> Adding time constraints to mcmctree tree
mcmc2tree -> Get the tree with internal node from mcmctree output
mcmctree_out -> Parse MCMCTree produced .out file
Phylo-related stats
PhyloBiAssoc -> A wrapper for binaryPGLMM test