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    25 repositories

    • dockerfiles

      Public
      This repository contains Docker files for the images maintained by the Phenotypic Evolution Group at the Institute for Molecular and Cell Biology / Instituto de Investigação e Inovação em Saúde da Universidade do Porto.
      bioinformaticsbioinformatics-containersdocker-files
      Dockerfile
      •
      Apache License 2.0
      •14•46•0•16•Updated Oct 7, 2024Oct 7, 2024

    • bdip

      Public
      CSS
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • ipssa

      Public
      IPSSA (Integrated Positively Selected Sites Analyses): a Compi pipeline for to automatically identify positively selected amino acid sites using CodeML, omegaMap, and FUBAR.
      dockerdockerfilesgenomicsproteomicsreproducibilitybioinformatics
      Shell
      •
      Other
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • auto-pss-genome

      Public
      Auto-PSS-Genome (Automatic Positively Selected Sites Genome) is a Compi pipeline to automatically identify positively selected amino acid sites using three different methods, namely CodeML, omegaMap, and FUBAR in complete genomes (FASTA files containing all coding sequences).
      Shell
      •
      Other
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • auto-phylo

      Public
      A Docker-based pipeline maker for phylogenetic studies
      Dockerfile
      •1•1•0•0•Updated Sep 5, 2024Sep 5, 2024

    • phylogenetic-tree-collapser

      Public
      Phylogenetic Tree Collapser
      Shell
      •
      Other
      •0•2•0•0•Updated Jul 31, 2024Jul 31, 2024

    • auto-p2docking-docs

      Public
      Read the docs for auto-p2docking
      Python
      •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • auto-p2docking

      Public
      0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • cport

      Public
      CPORT is a Consensus Prediction Of interface Residues in Transient complexes used to predict protein-protein interface residues.
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated May 21, 2024May 21, 2024

    • evoppi-querier

      Public
      A program to make queries to the EvoPPI web server.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • auto-phylo-docs

      Public
      Read the docs for auto-phylo
      Python
      •0•0•0•0•Updated Apr 9, 2024Apr 9, 2024

    • auto-phylo-pipeliner

      Public
      A GUI to design auto-phylo pipelines.
      Python
      •
      Other
      •0•0•0•0•Updated Oct 27, 2023Oct 27, 2023

    • drosophila-inversion-breakpoints

      Public
      Drosophila Inversion Breakpoints (DIB) pipeline.
      Shell
      •
      Other
      •1•0•0•0•Updated Oct 25, 2023Oct 25, 2023

    • seda-pipeline-phylogenomics-study

      Public
      A SEDA-Compi protocol for for a phylogenomics study.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • seda-pipeline-phylogenetics-datasets

      Public
      A SEDA-Compi protocol for preparing datasets for large scale phylogenetic analyses.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 15, 2023Sep 15, 2023

    • seda-pipeline-protein-family-members

      Public
      A SEDA-Compi protocol for obtaining protein family members.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 15, 2023Sep 15, 2023

    • classify

      Public
      Image classification using PyTorch
      Python
      •0•0•0•0•Updated Jun 13, 2023Jun 13, 2023

    • orthologs-finder

      Public
      Commands to retrieve orthologous genes from DIOPT or Ensembl.
      Shell
      •
      MIT License
      •1•1•0•0•Updated Oct 17, 2022Oct 17, 2022

    • cga

      Public
      CGA (Conserved Genome Annotation) is a Compi pipeline to efficiently perform CDS annotations by automating the steps that researchers usually follow when performing manual annotations.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 9, 2022Sep 9, 2022

    • pss-genome-fs

      Public
      GenomeFastScreen: a Compi pipeline for Fast Screening of PSS (Positively Selected Sites).
      Dockerfile
      •
      Other
      •0•1•0•0•Updated Sep 2, 2022Sep 2, 2022

    • pss-fs

      Public
      FastScreen: a Compi pipeline for Fast Screening of PSS (Positively Selected Sites).
      pipelinepositive-selectioncodemlfubarcompifasttree
      Shell
      •
      Other
      •1•1•0•0•Updated Sep 2, 2022Sep 2, 2022

    • haddock-tools

      Public
      Python
      •
      Apache License 2.0
      •17•0•0•0•Updated Jan 11, 2022Jan 11, 2022

    • check-cds

      Public
      CheckCDS: a compi pipeline to produce valid CDS files.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jun 14, 2021Jun 14, 2021

    • two-way-blast

      Public
      A Compi pipeline for finding orthologs using a two-way BLAST approach.
      dockerpipelineblastsequenceorthologscompi
      Dockerfile
      •
      Other
      •0•1•0•0•Updated Apr 28, 2021Apr 28, 2021

    • whiscy

      Public
      New version of the code of the Whisky bioinformatic predictor of protein-protein interfaces
      R
      •2•0•0•0•Updated May 17, 2019May 17, 2019