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gentrius_2023sm

Data and Code for the manuscript "Identifying equally scoring trees in phylogenomics with incomplete data using Gentrius"

iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

lpor_revolver

sequence evolution from SDR protein sequence towards LPOR

matrixsimulator

A simulator to generate 0-1 matrices, while controlling for various characteristics such as the number and spread of 0's across matrix, minimum and maximum numbers of 0/1 in each row/column, and others.

nextflow_gentrius_sim

olgachern.github.io

Personal website: https://olgachern.github.io/

scripts_evo_gen_brain_evo

scripts used for brain-evo project: data collection, data pre-processing, preparation of alignments, model selection, tree inference, computation of dN/dS, parsing and formatting output for downstream analysis, results visualisation at different steps of the analysis. Scripts have hard-coded paths and file names, mainly to keep track, where the actual data (inputs and results) are located.

scripts_naive_terrace_analysis

scripts to perform naive terrace analysis by analysing all trees in the corresponding tree space