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201502_basicphylogenetics

Basic command-line tutorial for phylogenetic analysis

2021_amphistegina_rna-seq

barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

complete-python-3-bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

dnapipete

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

jml

Testing hybridization using species trees

mcscanx

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

metabolic

A scalable high-throughput metabolic and biogeochemical functional trait profiler

phylofisher

PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.

phylogenomic-pipeline-for-microbial-eukaryotes

phylotol

seqtodna

This is the workflow used for recontruction of rDNA and target contigs from high-throughput sequencing data using reference sequences

springer_methods_chapter

Scripts for phylogenomics

starbeast2

Faster multispecies coalescent inference using multilocus data

tefinder

A bioinformatics tool for detecting novel transposable element insertions