Karen Siu Ting's repositories
catsequences
A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses
concatabomination
Pipeline for the method described in: Siu-Ting K., Pisani D., Creevey C.J., Wilkinson M. (2015). Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction. Systematic Biology.
Fix_models_RAxML
This repository contains modified codes of the master RAxML to make phylogenetic inferences fixing the model.
clan_check
Check trees for compatibility with defined groupings in unrooted trees - "The incontestable clan test"
convert_fasta_files
Shell scripts for quick modification of fasta files for convert these into 1 line formats. This makes fasta files easier for parsing into other pipelines that involve filtering or selecting sequences. At the moment these scripts convert to: fasta to 1-line fasta, and fasta to 1-line phylip format.
McCann_etal_Snail_microbiome
Scripts used for the Snail Microbiome analysis
Pipeline_for_eDNA_with_Nanopore
Set of scripts to run Kraken 2 and other tools onto Nanopore data (or other sequencing data in general that is in fastq).