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Updated: Sep 6, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases
Ohana Y A Costa1, Mattias de Hollander1,2, Eiko E Kuramae1,3
1Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands.
Abstract:
The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.
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