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One command line auto reconstruct phylogenetic tree.

Project description

PyPI version Docs License

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

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

https://raw.githubusercontent.com/yangfangs/physpetools/master/docs/docs/img/PhySpeTree_work_follow.png

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
  1. 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.

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

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

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