Software
Pipeline for taxonomic profiling of metagenomics reads
metaBIT (Louvel, Der Sarkissian et al. 2016)
It takes trimmed reads (fastq) as input and performs various taxonomical analyses. It relies on MetaPhlAn2 for the taxonomic proportions and was written in Python 2.7 and R.
I also developed phylogenetic tools for my personal usage:
Multipurpose phylogenetic tools
Reconciliation
Genarium: reconcile polytomic species trees with amalgamated gene trees.
Miscellaneous
wikipedia2phylo: parse phylogenetic trees from Wikipedia pages
Species_markovi: generate random species names.
pdfmetadata_from_zotero: update PDF metadata from your Zotero database.