clipkit 0.1.1

Alignment trimming software for phylogenetics.

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ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

If you found clipkit useful, please cite ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. bioRxiv. doi: 10.1101/2020.06.08.140384.

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Guide

Quick Start
Advanced Usage
Performance Assessment

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Quick Start

1) Installation

To install, use the following commands:

pip install clipkit # Currently not implemented. This will be functional by June 11th 2020.

To install from source, use the following commands:

git clone https://github.com/JLSteenwyk/ClipKIT.git
cd ClipKIT/
make install

If you run into permission errors when executing make install, create a virtual environment for your installation:

git clone https://github.com/JLSteenwyk/ClipKIT.git
cd ClipKIT/
python -m venv .venv
source .venv/bin/activate
make install

Note, the virtual environment must be activated to use clipkit.

2) Usage

To use ClipKIT in its simpliest form, execute the following command:

clipkit <input>

Output file with the suffix ".clipkit"

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Advanced Usage

This section describes the various features and options of ClipKIT.
- Modes
- Output
- Log
- Complementary
- All options

Modes

ClipKIT can be run with five different modes (gappy, kpic, kpic-gappy, kpi, and kpi-gappy), which are specified with the -m/--mode argument.
Default: 'gappy'

• gappy: trim all sites that are above a threshold of gappyness (default: 0.9)
  
• kpic (alias: medium): keep only parismony informative and constant sites
  
• kpic-gappy (alias: medium-gappy): a combination of kpic- and gappy-based trimming
  
• kpi (alias: heavy): keep only parsimony informative sites
  
• kpi-gappy (alias: heavy-gappy): a combination of kpi- and gappy-based trimming
  

# gappy-based trimming
clipkit <input>
clipkit <input> -m gappy

# kpic-based trimming
clipkit <input> -m kpic
clipkit <input> -m medium

# kpic- and gappy-based trimming
clipkit <input> -m kpic-gappy
clipkit <input> -m medium-gappy

# kpi-based trimming
clipkit <input> -m kpi
clipkit <input> -m heavy

# kpi- and gappy-based trimming
clipkit <input> -m kpi-gappy 
clipkit <input> -m heavy-gappy

Output

By default, output files will have the same name as the input file with the suffix ".clipkit" appended to the name. Users can specify output file names with the -o option.

# specify output
clipkit <input> -o <output>

Log

It can be very useful to have information about the each position in an alignment. For example, this information could be used in alignment diagnostics, fine-tuning of trimming parameters, etc. To create the log file, use the -l/--log option. Using this option will create a four column file with the suffix '.clipkit.log'. Default: off

• col1: position in the alignment (starting at 1)
• col2: reports if site was trimmed or kept (trim or keep, respectively)
• col3: reports if the site is constant or not (Const or nConst), parsimony informative or not (PI or nPI), or neither (nConst, nPI)
• col4: reports the gappyness of the position (number of gaps / entries in alignment)

clipkit <input> -l

Output file with the suffix ".clipkit.log"

Complementary

Having an alignment of the sequences that were trimmed can be useful for other analyses. To obtain an alignment of the sequences that were trimmed, use the -c/--complementary option. Default: off

clipkit <input> -c

Output file with the suffix ".clipkit.complementary"

All options

Option	Usage and meaning
-h/--help	Print help message
-v/--version	Print software version
-o/--output	Specify output file name
-m/--modes	Specify trimming mode. Default: gappy
-g/--gaps	Specify gappyness threshold (between 0 and 1). Default: 0.9
-if/--input_file_format	Specify input file format*. Default: auto-detect
-of/--input_file_format	Specify output file format*. Default: input file type
-l/--log	Create a log file. Default: off
-c/--complementary	Create a complementary alignment file. Default: off

*Acceptable file formats include: fasta, clustal, maf, mauve, phylip, phylip-sequential, phylip-relaxed, stockholm

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Performance Assessment

In brief, performance assessment and comparison of multiple trimming alignment software revealed that ClipKIT with nearly any mode is a top-performing software. Here, we provide greater detail into the empirical datasets used to assess alignment trimming performance.

ClipKIT is a top-performing software for trimming multiple sequence alignments. Across a total of 138,152 multiple sequence alignments (MSAs) from empirical (left) and simulated (right) datasets, desirability-based integration of accuracy and support metrics per MSA facilitated the comparison of relative software performance and revealed ClipKIT is a top-performing software. MSA trimming approaches are ordered along the x-axis from the highest-performing software to the lowest-performing software according to average desirability-based rank. Abbreviations of trimmers and parameters are as follows: ClipKIT: g = gappy mode; ClipKIT: kc = kpic; ClipKIT: kcg = kpic-gappy; ClipKIT: k = kpi mode; ClipKIT: kg = kpi-gappy mode; BMGE = BMGE default; BMGE 0.3 = 0.3 entropy threshold; BMGE 0.7 = 0.7 entropy threshold; trimAl: s = strict; trimAl: sp = strictplus; Noisy = default; Gblocks = default; No trim = no trimming.

For additional performance details, please see the manuscript ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. bioRxiv. doi: 10.1101/2020.06.08.140384.

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Authors

• Jacob Steenwyk
  
• Thomas Buida
  
• Yuanning Li
• Xing-Xing Shen
• Antonis Rokas

Developers

• Jacob Steenwyk
  
• Thomas Buida