marco-mariotti Goto Github PK
Name: Marco Mariotti
Type: User
Company: Universitat de Barcelona
Bio: Principal investigator at Universitat de Barcelona
Location: Barcelona, Catalonia, Spain
Name: Marco Mariotti
Type: User
Company: Universitat de Barcelona
Bio: Principal investigator at Universitat de Barcelona
Location: Barcelona, Catalonia, Spain
Collection of bioinformatics tools related to alignments and phylogenetic trees
Wrapper to submit jobs to a SGE cluster. Can split large jobs in clusters or submit array jobs.
Convenient functions for everyday bioinformatics
convenient python functions for everyday use of terminal
Search and download Ensembl data such as genome assemblies and gene annotations
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.
Utility to extend genomic intervals into complete open reading frames
Python classes to iterate through files in chunks
Fishers Exact Test for Python (Cython)
Tools to build your own copy of selected entries form the ncbi databases
Download a NCBI genome, process it with your own code, then trash it
PhylomeDB automated pipeline for reconstructing high-quality phylogenetic tree
Read, process, write multiple sequence alignments
Graphical environment for evolutionary analysis of coding sequence alignments
Performant Pythonic GenomicRanges
PyRanges as a DataFrame subclass.
Gene visualization package for dataframe objects generated with PyRanges
Utility to split shell commands into jobs, then submit them for computation to a queue of a SGE or Slurm cluster.
Prediction of selenocysteine tRNA (tRNA-Sec) in genomes
Selenoprofiles is a pipeline for profile-based protein finding in genomes. It is suitable also (but not only) for selenoproteins
Gene finding pipeline for selenoprotein and selenocysteine machinery
Profile alignments to be searched with selenoprofiles_4
Extends the pyranges module with operations on joined genomic intervals (e.g. exons of same transcript)
ETE4 module for exploration of quantitative data along a species tree
the Tree Data Explorer - interactive platform for analysis of comparative omics
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 1.4
Twinstop identifies selenoproteins in close related transcriptomes
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