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Phylogenetics

RAxML

GCATemplates

RAxML homepage

To see the available versions, type the following on the command line:

module spider RAxML

RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.

AAF

GCATemplates

AAF homepage

Use the module spider command to see the available versions of AAF:

module spider AAF

AAF (alignment and assembly-free) is a free software package that reconstructs phylogeny from next-generation sequencing data without assembly and alignment.

It takes raw sequencing reads from each sample altogether and generates a distance matrix based on the proportion of shared k-mers between each sample and reconstruct a phylogeny based on the distance matrix.

If you are running aaf_distance.py with > 10 cores and the command is failing with a message like IndexError: list index out of range then use fewer cores such as -t 5

IQ-TREE

GCATemplates available: no

IQ-TREE homepage

Efficient phylogenomic software by maximum likelihood

When running using all 20 cores (#BSUB -n 20) on a 64 GB or 256 GB node, use the following in your job script:

module load IQ-TREE/1.5.5-GCCcore-6.3.0
OMP_NUM_THREADS=20

If you need to run on xlarge nodes (1 TB or 2 TB nodes) and you are using #BSUB -n 40 then use the following in your job script:

module load Westmere
module load IQ-TREE/1.5.5-GCCcore-6.3.0
OMP_NUM_THREADS=40

Use the following command to run IQ-TREE

iqtree-omp

BPGA

GCATemplates available: no

BPGA homepage

BPGA is an ultra-fast software package that provides comprehensive pan genome analysis of microorganisms. In addition to all types of routine pan genomic analyses (Pan genome Profiles, Pan/Core Phylogeny etc.), BPGA includes a number of novel downstream analysis features like Exclusive Gene Family Analysis, Atypical GC Content Analysis, Subset Analysis, MLST based on housekeeping genes and KEGG Distribution etc.

BPGA creates files in the installation directory so you will have to open the .tar.gz package in your working directory for each project.

You can use the following commands to run BPGA from within your working directory in your $SCRATCH space.

You can name your working directory anything you want, in this example it is $SCRATCH/bpga_project

module purge
module load USEARCH/10.0.240-i86linux32
module load LibTIFF/4.0.7-GCCcore-6.3.0
module load glibc/2.14
module load gnuplot/4.6.6-GCCcore-6.3.0-Python-2.7.12-bare
module load Ghostscript/9.21-GCCcore-6.3.0-Python-2.7.12-bare
module load Python/2.7.12-intel-2017A

mkdir $SCRATCH/bpga_project
cd $SCRATCH/bpga_project
cp /sw/eb/sources/b/BPGA/BPGA-1.3-linux-x86_64-0-0-0.tar.gz ./
tar xzf BPGA-1.3-linux-x86_64-0-0-0.tar.gz
cd BPGA-1.3-linux-x86_64-0-0-0/BPGA-Version-1.3/bin
ln -s $EBROOTUSEARCH/bin/usearch
chmod +x BPGA-Version-1.3
./BPGA-Version-1.3

When running BPGA, it will prompt you for the full path to the directory that has your input files

PhyloNetworks

GCATemplates available: no

PhyloNetworks homepage

PhyloNetworks is a Julia package for the manipulation, visualization, inference of phylogenetic networks, and their use for trait evolution.

PICRUSt

GCATemplates available: no

PICRUSt homepage

PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.

module load PICRUSt/1.1.3-intel-2017A-Python-2.7.12

If you need to use R with the ape package, you can load the following R_tamu version

module load R_tamu/3.3.2-intel-2017A-Python-2.7.12-default-mt`

PICRUSt2 is available using Anaconda

module load Anaconda/3-5.0.0.1
source activate picrust2-2.3.0_b

GCATemplates available: no

PIECRUSt homepage

PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.

# GRACE 

module load Anaconda3/2021.05
source activate /sw/hprc/sw/Anaconda3/2021.05/envs/picrust2_2.4.1

PhyloSNP

GCATemplates available: no

PhyloSNP homepage

PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data.

Additionally, PhyloSNP can either generate a shortened concatenated genome from the SNPs or generate a concatenated genome from contigs generated from the SNPs and a specified number of base pairs around each SNP.

module load PhyloSNP/20140203-GCC-9.3.0

PhyloSNP works best with bacterial genomes. For larger genomes or projects with many samples, use the shrunk-genomes.pl script in the PhyloSNP module.

SNPhylo

GCATemplates available: no

SNPhylo homepage

SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP data.

module load SNPhylo/2018.10.05-foss-2020a-Python-2.7.18

SNPhylo works best with large genomes such as the human genome. Smaller genomes such as bacterial and fungal genomes probably will not have enough variants (5000 minimum) after the filtering step.

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