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biotree_tools

Collection of bioinformatics tools related to alignments and phylogenetic trees

cluster_job

Wrapper to submit jobs to a SGE cluster. Can split large jobs in clusters or submit array jobs.

easybioinfo

Convenient functions for everyday bioinformatics

easyterm

convenient python functions for everyday use of terminal

ensembl_assembly

Search and download Ensembl data such as genome assemblies and gene annotations

ete

ETE is a Python programming toolkit for building, comparing, annotating, manipulating and visualising trees. It provides both a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

extend_orfs

Utility to extend genomic intervals into complete open reading frames

fastagetseq

fastatools

file_chunk_iterators

Python classes to iterate through files in chunks

fishers_exact_test

Fishers Exact Test for Python (Cython)

ncbi_db

Tools to build your own copy of selected entries form the ncbi databases

ncbi_single_use_genome

Download a NCBI genome, process it with your own code, then trash it

orf_tools

phylomizer

PhylomeDB automated pipeline for reconstructing high-quality phylogenetic tree

pyaln

Read, process, write multiple sequence alignments

pycodeml

Graphical environment for evolutionary analysis of coding sequence alignments

pyranges

Performant Pythonic GenomicRanges

pyranges_1.x

PyRanges as a DataFrame subclass.

qjob

Utility to split shell commands into jobs, then submit them for computation to a queue of a SGE or Slurm cluster.

secmarker

Prediction of selenocysteine tRNA (tRNA-Sec) in genomes

selenoprofiles

Selenoprofiles is a pipeline for profile-based protein finding in genomes. It is suitable also (but not only) for selenoproteins

selenoprofiles4

Gene finding pipeline for selenoprotein and selenocysteine machinery

selenoprotein_profiles

Profile alignments to be searched with selenoprofiles_4

tiedpyranges2

Extends the pyranges module with operations on joined genomic intervals (e.g. exons of same transcript)

treedex

ETE4 module for exploration of quantitative data along a species tree

treedex_pyqt4

the Tree Data Explorer - interactive platform for analysis of comparative omics

trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 1.4

twinstop

Twinstop identifies selenoproteins in close related transcriptomes