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ontology-development-kit

Bootstrap an OBO Library ontology

orange3

:tangerine: Orange 3 data mining suite: http://orange.biolab.si

orthofinder

Phylogenetic orthology inference for comparative genomics

ortholog-finder-tool

Project aim is to find the most relevant functional protein to a given protein all used species. Project will evolve in time.

otunetworks

otusummary

R package of 'otuSummary'

owc_mags_genome_annotation

May use DRAM et al. tools to annotate genomes or MAGs

owc_metat_analysis2019

metaT_analysis of the OWC wetland dataset, 2019, mapping, quantification,

owc_sulfate_reduction

this is a side story on sulfate reduction in OWC wetland based on 16S, biogeochemical, metaG, metaT

owc_wetland2018_16s

methane cycle in 4D

pangenomics

Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.

panseq

Pan-genomic sequence analysis

parallel-meta-suite

phagcn

GCN classifier for phage taxanomy classification

phagcn2.0

pheatmap

Pretty heatmaps

phisdector

phispy

Prediction of prophages from bacterial genomes

phyloflash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

phylogenetic_tree_learnning

learn phylogenetic tree building and log of commands used for tree

phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

phylorank

Assign taxonomic ranks based on evolutionary divergence.

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

picrust

Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests

picrust2

Code, unit tests, and tutorials for running PICRUSt2

pilon

Pilon is an automated genome assembly improvement and variant detection tool

pipeline

metagenomic analysis server pipeline scripts

planet-microbe-ontology

plasforest

A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes

plotluck

R tool for automated creation of ggplots. Examines one, two, or three variables and creates, based on their characteristics, a scatter, violin, box, bar, density, hex or spine plot, or a heat map. Also automates handling of observation weights, log-scaling of axes, reordering of factor levels, and overlays of smoothing curves and median lines.