Phylogenomic analysis of the phylum Nematoda

Supplementary data for the manuscript entitled "Phylogenomic analysis of the phylum Nematoda: conflicts and congruences with morphology- and 18S rRNA-based phylogenies and classifications."

CONTACT INFORMATION

Oleksandr Holovachov
Swedish Museum of Natural History
Box 50007, SE-104 05, Stockholm, Sweden
oleksandr.holovachov@nrm.se



DATA OVERVIEW

1_TRICHINELLIDA: This folder contains subfolders containing files generated at the various analysis stages for the TRICHINELLIDA dataset. Directory structure for this dataset follows the structure described under “FOLDER DESCRIPTION” below.

2_SPIRURINA: This folder contains subfolders containing files generated at the various analysis stages for the SPIRURINA dataset. Directory structure for this dataset follows the structure described under “FOLDER DESCRIPTION” below.

3_TYLENCHINA: This folder contains subfolders containing files generated at the various analysis stages for the TYLENCHINA dataset. Directory structure for this dataset follows the structure described under “FOLDER DESCRIPTION” below.

4_RHABDITINA: This folder contains subfolders containing files generated at the various analysis stages for the RHABDITINA dataset. Directory structure for this dataset follows the structure described under “FOLDER DESCRIPTION” below.

5_NEMATODA: This folder contains subfolders containing files generated at the various analysis stages for the full NEMATODA dataset. Directory structure for this dataset follows the structure described under “FOLDER DESCRIPTION” below.



FOLDER STRUCTURE

01_INPUT: This folder contains the proteomes used for inferring orthology using proteinortho.

02_PRTNRTH: Output files from proteinortho.

03_INPUT_50: List of all orthologs (fasta format) with more than 50% of the included taxa.

04_MAFFT: All mafft-aligned orthologs.

05_ALISCORE: All aliscore output text files.

06_ALICUT: All cleaned/filtered alignments following aliscore/alicut run.

07_IQTREE: Maximum likelihood analysis inferred using IQ-TREE.

08_PHPPRNR: PhyloPyPruner output.

09_RAXML: Maximum likelihood analysis using RAxML on the supermatrix file generated after PhyloPyPruner.

10_IQTREE: Output of Maximum likelihood analysis using IQTREE on the supermatrix.

11_IQTREE: Output of Maximum likelihood analysis using IQTREE on the individual orthogroups after PhyloPyPruner. For ASTRAL species tree inference.

12_ASTRAL: Output of ASTRAL analysis.

SCRIPT: The script used for the entire analysis from steps 01–12. To run this script, all the above folders need to be created. The script should be placed and run from within the '03_INPUT_50' folder.