PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees

PhySpeTree is implemented in Python language (supports Python2.7+ and Python3+), designed for Linux systems (docker for Windows OS or Mac OS).

Documents: PhySpeTree documentation.

• Introduction
• PhySpeTree workflow
• Features
• Install
• Usage
  • autobuild
    • autobuild options
    • Advance options
  • build
    • build options
  • combine
    • combine options
  • iview
    • iview options
  • check
    • check options
• Frequently Asked Questions (FAQ)

Introduction

Understanding phylogenetic relationships between different species is crucial for evolutionary studies. Reconstructing the phylogenetic species tree, a branching diagram, is particularly useful in inferring evolutionary relationships. For example, the tree-of-life provides a remarkable view of organizing principles of the biological world. So, the exact species tree to be reconstructed is necessary, but the process of reconstructing the species or gene tree is very tedious.

Here, we developed an easy-to-use package named PhySpeTree that is convenient to reconstruct species trees by one command line. Two independent pipelines were included by using the most adopted small subunit ribosomal RNA (SSU rRNA) and concatenated highly conserved proteins (HCP), respectively. A distinct advantage is that users only need to input species names and PhySpeTree automatically downloads and analyzes sequences of SSU rRNA or HCP from about 4,000 organisms.

PhySpeTree workflow

PhySpeTree workflow includes the following steps:

• ① Automatic tree reconstruction.
• ② Processing user-defined fasta files for unannotated organisms.
• ③ Reconstructing species trees with unannotated organisms.

Features

• Inputs only include species names.
• One command line to build trees.
• HCP and SSU rRNA methods.
• Combine trees.
• View trees with iTOL.
• Versatile software with adjustable parameters.

Install

1. PyPI

$ pip install PhySpeTree

or download PhySpeTree and install:

$ pip install PhySpeTree-*.tar.gz

To upgrade to latest version:

$ pip install --upgrade PhySpeTree

2. GitHub

$ git clone git@github.com:yangfangs/physpetools.git
$ cd physpetools
$ python setup.py install

or download and install:

$ pip install physpetools-*.tar.gz

Usage

autobuild

The input of autobuild module is a TXT file containing abbreviated species names, for example organism example list.

Use autobuild in command line like this:

$ PhySpeTree -i organism_example_list.txt [options]*

autobuild options

-h	Print help message and exits.
-i	Input a TXT file containing abbreviated species names.
-o	A directory to store outputs. The default is "Outdata".
-t	Number of processing threads (CPUs). The default is 1.
-e	FASTA format files to extend the tree with the --ehcp or --esrna option.
--hcp	HCP (highly conserved protein) method (default).
--ehcp	HCP method with extended HCP sequences.
--srna	SSU method.
--esrna	SSU rRNA method with extended SSU rRNA sequences.

Advance options

Advanced options of internal software called in PhySpeTree can be set. These options are enclosed in single quotes and start with a space.

Here is an example of setting RAxML advanced options by --raxml_p:

$ PhySpeTree autobuild -i organism_example_list.txt -o test --srna --raxml --raxml_p ' -f a -m GTRGAMMA  -p 12345 -x 12345 -# 100 -n T1'

--muscle	Multiple sequence alignment by MUSCLE (default).
--muscle_p	Set Muscle advance parameters. The default is -maxiter 100, please see MUSCLE Manual. -maxiter maximum number of iterations to run is set 100.
--clustalw	Multiple sequence alignment by clustalw2.
--clustalw_p	Set clustalw2 advance parameters. Here use clustalw default parameters, please see Clustalw Help.
--mafft	Multiple sequence alignment by mafft.
--mafft_p	Set mafft advance parameters. Here use mafft default parameters, please see mafft algorithms.
--gblocks	Trim by Gblocks.(default)
--gblocks_p	Set Gblocks advance parameters, please see Gblocks documentation. -t Choice type of sequence(default). -e Generic File Extension. PhySpeTree set default is "-gbl1".
--trimal	Trim by trimal.
--trimal_p	Set trimal advance parameters, please see trimal command line.
--raxml	Reconstruct phylogenetic tree by RAxML (default).
--raxml_p	Set RAxML advanced parameters. The default is -f a -m PROTGAMMAJTTX -p 12345 -x 12345 -# 100 -n T1, please see RAxML Manual. -f select algorithm. The PhySpeTree default set is a, rapid Bootstrap analysis and search for best­scoring ML tree in one program run. -m Model of Binary (Morphological), Nucleotide, Multi­State, or Amino Acid Substitution. The PhySpeTree default set is PROTGAMMAJTTX. -p Specify a random number seed for the parsimony inferences. The physep default set is 12345. -x Specify an integer number (random seed) and turn on rapid bootstrapping. The PhySpeTree default set is 12345. -N The same with -# specify the number of alternative runs on distinct starting trees. The PhySpeTree default set is 100.
--fasttree	Reconstruct phylogenetic tree by FastTree.
--fasttree_p	Set FastTree advance parameters, please see FastTree.
--iqtree	Reconstruct phylogenetic tree by iqtree.
--iqtree_p	Set iqtree advance parameters, please see IQ-TREE.

build

The build module is used to reconstruct species trees with manually prepared sequences. Advanced options are the same as autobuild module.

Use build in command line to reconstruct phylogenetic tree:

• build phylogenetic tree by multiple method:

$ PhySpeTree build -i example_hcp -o output --multiple

• build phylogenetic tree by SSU rRNA method:

$ PhySpeTree build -i example_16s_ssurna.fasta -o output --single

build options

-h	Print help message and exits.
-i	Input a TXT file containing abbreviated species names.
-o	A directory to store outputs. The default is "Outdata".
-t	Number of processing threads (CPUs). The default is 1.
--multiple	Specify concatenate highly conserved protein method to reconstruct phylogenetic tree. The default method.
--single	Use SSU rRNA data to reconstruct phylogenetic tree.

combine

The combine module is used to combine trees generated from different methods. It contains two steps, at first merge different tree files into the same file. You can use cat bash command in the Linux system, for example:

$ cat tree1.tree tree2.tree > combineTree.tree

Then, use combine

$ PhySpeTree PhySpeTree combine -i combineTree.tree [options]*

combine options

-h	Print help message and exits.
-i	Input PHYLIP format file containing multiple trees.
-o	Output directory. The default is "combineTree".
--mr	Majority rule trees..
--mre	Extended majority rule trees.
--strict	Strict consensus trees.
--supertree	Use Spr_Supertree combining conflicting evolutionary histories that are due to lateral gene transfer (LGT).

iview

PhySpeTree provides the iview module to annotate taxonomic information (kingdom, phylum, class, or order) of output trees and to generate configure files linked to iTol.

Use iview in command line like this:

$ PhySpeTree iview -i organism_example_list.txt --range

iview options

-h	Print help message and exits.
-i	Input a TXT file containing abbreviated species names.
-o	A directory to store outputs. The default is "iview".
-r	Annotating labels with ranges by kingdom, phylum, class or order. The default is phylum.
-c	Annotating labels without ranges by kingdom, phylum, class or order. The default is phylum.
-a	Colored ranges by users assign, users can choice from [kingdom, phylum, class and order].
-l	Change species labels from abbreviated names to full names.

check

The check module is used to check whether input organisms are in pre-built databases.

$ PhySpeTree check -i organism_example_list.txt -out check --ehcp

check options

-h	Print help message and exits.
-i	Input a TXT file containing abbreviated species names.
-o	A directory to store outputs. The default is "check".
--hcp	Check whether organisms are supported in the KEGG database.
--ehcp	Check input organisms prepare for extend autobuild tree module.
--srna	Check whether organisms are supported in the SILVA database.

Frequently Asked Questions (FAQ)

1.What is the input of PhySpeTree?

Users only need to prepare a TXT file containing KEGG abbreviated species names. For example, organism example list.

2.How to explain PhySpeTree outputs?

PhySpeTree returns two folders, Outdata contains the output species tree and temp includes temporary data. Files in temp can be used to check the quality of outputs in each step. If HCP method (--hcp) is selected, the temp folder includes:

• conserved_protein: highly conserved proteins retrieved from the KEGG database.
• alignment: aligned sequences.
• concatenate: concatenated sequences and conserved blocks.

If SSU rRNA method (--srna) is selected, the temp folder includes:

• rna_sequence: SSU rRNA sequences retrieved from the SILVA database.
• rna_alignment: aligned sequences and conserved blocks.

3.What classes of HCP are selected?

PhySpeTree uses 31 HCP without horizontal transferred genes according to Ciccarelli et al..

cite:

Ciccarelli F D, Doerks T, Von Mering C, et al. Toward automatic reconstruction of a highly resolved tree of life[J]. science, 2006, 311(5765): 1283-1287.

The 31 HCP and corresponding KEGG KO number are shown in the following table:

Protein Names	Eukaryotes KO	Prokaryotes KO
DNA-directed RNA polymerase subunit alpha	K03040	K03040
Ribosomal protein L1	K02865	K02863
Leucyl-tRNA synthetase	K01869	K01869
Metal-dependent proteases with chaperone activity	K01409	K01409
Phenylalanine-tRNA synthethase alpha subunit	K01889	K01889
Predicted GTPase probable translation factor	K06942	K06942
Preprotein translocase subunit SecY	K10956	K10956
Ribosomal protein L11	K02868	K02867
Ribosomal protein L13	K02873	K02871
Ribosomal protein L14	K02875	K02874
Ribosomal protein L15	K02877	K17437
Ribosomal protein L16/L10E	K02866	K02872
Ribosomal protein L18	K02883	K02882
Ribosomal protein L22	K02891	K02890
Ribosomal protein L3	K02925	K02906
Ribosomal protein L5	K02932	K02931
Ribosomal protein L6P/L9E	K02940	K02939
Ribosomal protein S11	K02949	K02948
Ribosomal protein S15P/S13E	K02958	K02956
Ribosomal protein S17	K02962	K02961
Ribosomal protein S2	K02981	K02967
Ribosomal protein S3	K02985	K02982
Ribosomal protein S4	K02987	K02986
Ribosomal protein S5	K02989	K02988
Ribosomal protein S7	K02993	K02992
Ribosomal protein S8	K02995	K02994
Ribosomal protein S9	K02997	K02996
Seryl-tRNA synthetase	K01875	K01875
Arginyl-tRNA synthetase	K01887	K01887
DNA-directed RNA polymerase beta subunit	K03043	K03043
Ribosomal protein S13	K02953	K02952

4.How are SSU rRAN created?

The SSU rRAN sequences are created from the SILVA database (123.1 release). Sequences haven been truncated, which means unaligned nucleotides are removed.

5. How do I use PhySpeTree when I can't connect to the Internet?

When users can't connect to the Internet. They can download the HCP or SSU rRNA database to local and reconstruct species tree.

• SSU rRNA database: database16s.tar.gz
• HCP database: databasehcp.tar.gz

Use $ tar -zxvf database16s.tar.gz decompress the download database.

Use -db option setting the absolute path to decompression directory.

Cite: Fang, Y., Liu, C., Lin, J. et al. PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. BMC Evol Biol 19, 219 (2019). https://doi.org/10.1186/s12862-019-1541-x