SPDel: Comparing Species delimitation and statistics for DNA Barcoding datasets

SPdel is a pipeline to integrate different single-gene species delimitation methods. SPdel is designed to calculate statistics and compare MOTUs obtained by different methods (e.g. GMYC, PTP, bPTP, BIN, etc).

Requirement:

• Anaconda
• Git

Installation:

Open Anaconda prompt or terminal:

conda env create -f environment.yml
conda activate spdel 

Before use jupyter version for first time:

python -m ipykernel install --user --name spdel

Overview

The pipeline SPdel can run PTP, BPTP and GMYC analyses locally in your computer using original codes and then parse the results. Also, SPdel can interpretate output files from PTP and bPTP web server (https://species.h-its.org/) or python distribution (https://github.com/zhangjiajie/PTP). For GMYC the pipeline works with the outfile from python version (https://github.com/zhangjiajie/pGMYC), but you can use the R version or the web server (https://species.h-its.org/gmyc/) and include your results using -X option. Please check the example files included.

Please cite original authors of each species delimitation used.

How to Use:

The sequences name should be separate for "_" (e.g. Genus_species_individual) or use -N option for rename sequences

In this example we will use the LA_nominal.fasta dataset included in data folder.

Calculates genetic distances for nominal species

SPdel.py path/Megaleporinus_COI.fasta -n

Calculate ABGD, ASAP, PTP, bPTP and GMYC locally and perfom genetic distances analyses

SPdel.py path/Megaleporinus_COI.fasta -n -A -S -P -T -G -t path/Megaleporinus_tree.nwk

Calculates genetics distances from MOTUs delimited for BIN using outfiles calculated outside the pipeline

SPdel.py path/Megaleporinus_COI.fasta -B path/BIN_List.txt -t path/Megaleporinus_tree.nwk

Compare analyses previously calculated

SPdel.py path/Megaleporinus_COI.fasta -C Nominal,ABGD,ASAP,PTP,bPTP,GMYC -t path/Megaleporinus_tree.nwk

Calculate all analyses and compare the results

SPdel.py path/Megaleporinus_COI.fasta -n -A -S -P -T -G -B path/BIN_List.txt -t path/Megaleporinus_tree.nwk -C Nominal,ABGD,ASAP,PTP,bPTP,GMYC,BIN

Options:

-n           For nominal analysis.
-distance    Substitution model, k for K2p or p for p-distance (default=k)
-t           Specify the path of the input newick tree for PTP, bPTP and GMYC analysis.
-N           Specify the path of the text file including the nominal names for rename the sequences.
-A           ABGD analysis.
-S           ASAP analysis. 
-P           PTP analysis.
-T           bPTP analysis.
-M           mPTP analysis.    
-G           GMYC analysis.             
-X           Specify the path of the CSV file including the MOTUs names obtained from any external method (e.g. BIN).
-D           For Diagnostic character analysis.
-C           Specify the type of analisys to be compared, include n for nominal, p for PTP, t for bPTP, b for BIN, and any filename  used in X option for external MOTU lists. 
-code        Specify the genetic code used to test stop codon, VER or INV.

Options for nominal:

-gen         Position of the genus name in the sequence name when split by "_" (default=1).
-sp          Position of the species name in the sequence name when split by "_" (default=2)   

Options for bPTP

    -n_iter       Number of iteration for bPTP analysis (default=10000)
    -sample      Number of sampling for bPTP analysis (default=100)
    -burnin      Burnin for bPTP analysis (default=0.1)     

Options for diagnostic character:

-n_ind       Minimum number of individuals for species to be considered in the diagnostic character analysis (default=3)