tlynx-0.5.0: README.md
# The ELynx Suite
Version: 0.5.0.
Reproducible evolution made easy.
<p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>
A Haskell library and tool set for computational biology. The goal of ELynx is
reproducible research. Evolutionary sequences and phylogenetic trees can be
read, viewed, modified and simulated. The command line with all arguments is
logged consistently, and automatically. Data integrity is verified using SHA256
sums so that validation of past analyses is possible without the need to
recompute the result.
The Elynx Suite consists of library packages and executables providing a range
of sub commands.
The library packages are:
- **elynx-nexus:** Nexus file support.
- **elynx-markov:** Simulate multi sequence alignments along phylogenetic trees.
- **elynx-seq:** Handle evolutionary sequences and multi sequence alignments.
- **elynx-tools:** Tools for the provided executables.
- **elynx-tree:** Handle phylogenetic trees.
The executables are:
- **slynx:** Analyze, modify, and simulate evolutionary sequences.
- **tlynx:** Analyze, modify, and simulate phylogenetic trees.
- **elynx:** Validate and redo past analyses.
**ELynx is actively developed. We happily receive comments, ideas, feature
requests, and pull requests!**
# Installation
ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [Stack](https://docs.haskellstack.org/en/stable/README/).
1. Install Stack with your package manager, or directly from the web
page.
curl -sSL https://get.haskellstack.org/ | sh
2. Clone the ELynx repository.
git clone https://github.com/dschrempf/elynx
3. Navigate to the newly created `elynx` folder and build the binaries.
This will take a while.
stack build
4. Run a binary from within the project directory. For example,
stack exec tlynx -- --help
5. If needed, install the binaries.
stack install
The binaries are installed into `~/.local/bin/` which has to be added to the
[PATH](https://en.wikipedia.org/wiki/PATH_(variable)) environment variable. Then, they can be used directly.
# Documentation
Documentation is available on [Hackage](https://hackage.haskell.org/).
Libraries:
- [elynx-nexus](https://hackage.haskell.org/package/elynx-nexus)
- [elynx-markov](https://hackage.haskell.org/package/elynx-markov)
- [elynx-seq](https://hackage.haskell.org/package/elynx-seq)
- [elynx-tools](https://hackage.haskell.org/package/elynx-tools)
- [elynx-tree](https://hackage.haskell.org/package/elynx-tree)
Executables:
- [elynx](https://hackage.haskell.org/package/elynx)
- [slynx](https://hackage.haskell.org/package/slynx)
- [tlynx](https://hackage.haskell.org/package/tlynx)
# SLynx
Handle evolutionary sequences.
slynx --help | head -n -16
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
Analyze, and simulate multi sequence alignments.
Available options:
-h,--help Show this help text
-V,--version Show version
-v,--verbosity VALUE Be verbose; one of: Quiet Warning Info
Debug (default: Info)
-o,--output-file-basename NAME
Specify base name of output file
-f,--force Ignore previous analysis and overwrite existing
output files.
--no-elynx-file Do not write files for needed for reproducibility.
Available commands:
concatenate Concatenate sequences found in input files.
examine Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
filter-columns Filter columns of multi sequence alignments.
filter-rows Filter rows (or sequences) found in input files.
simulate Simulate multi sequence alignments.
sub-sample Sub-sample columns from multi sequence alignments.
translate Translate from DNA to Protein or DNAX to ProteinX.
Available sequence file formats:
- FASTA
Available alphabets:
- DNA (nucleotides)
- DNAX (nucleotides; including gaps)
- DNAI (nucleotides; including gaps, and IUPAC codes)
- Protein (amino acids)
- ProteinX (amino acids; including gaps)
- ProteinS (amino acids; including gaps, and translation stops)
## Concatenate
Concatenate multi sequence alignments.
slynx concatenate --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE
Concatenate sequences found in input files.
Available options:
-h,--help Show this help text
-V,--version Show version
-a,--alphabet NAME Specify alphabet type NAME
INPUT-FILE Read sequences from INPUT-FILE
-h,--help Show this help text
## Examine
Examine sequence with `slynx examine`.
slynx examine --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]
Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
Available options:
-h,--help Show this help text
-V,--version Show version
-a,--alphabet NAME Specify alphabet type NAME
INPUT-FILE Read sequences from INPUT-FILE
--per-site Report per site summary statistics
-h,--help Show this help text
## Filter
Filter sequences with `filer-rows`.
slynx filter-rows --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH]
[--shorter-than LENGTH] [--standard-characters]
Filter rows (or sequences) found in input files.
Available options:
-h,--help Show this help text
-V,--version Show version
-a,--alphabet NAME Specify alphabet type NAME
INPUT-FILE Read sequences from INPUT-FILE
--longer-than LENGTH Only keep sequences longer than LENGTH
--shorter-than LENGTH Only keep sequences shorter than LENGTH
--standard-characters Only keep sequences containing at least one standard
(i.e., non-IUPAC) character
-h,--help Show this help text
Filter columns of multi sequence alignments with `filter-columns`.
slynx filter-columns --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE
[--standard-chars DOUBLE]
Filter columns of multi sequence alignments.
Available options:
-h,--help Show this help text
-V,--version Show version
-a,--alphabet NAME Specify alphabet type NAME
INPUT-FILE Read sequences from INPUT-FILE
--standard-chars DOUBLE Keep columns with a proportion standard (non-IUPAC)
characters larger than DOUBLE in [0,1]
-h,--help Show this help text
## Simulate
Simulate sequences with `slynx simulate`.
slynx simulate --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
[-m|--mixture-model MODEL] [-e|--edm-file NAME]
[-p|--siteprofile-files NAMES]
[-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]
[-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]
(-l|--length NUMBER) [-S|--seed [INT]]
Simulate multi sequence alignments.
Available options:
-h,--help Show this help text
-V,--version Show version
-t,--tree-file Name Read tree from Newick file NAME
-s,--substitution-model MODEL
Set the phylogenetic substitution model; available
models are shown below (mutually exclusive with -m
option)
-m,--mixture-model MODEL Set the phylogenetic mixture model; available models
are shown below (mutually exclusive with -s option)
-e,--edm-file NAME Empirical distribution model file NAME in Phylobayes
format
-p,--siteprofile-files NAMES
File names of site profiles in Phylobayes format
-w,--mixture-model-weights "[DOUBLE,DOUBLE,...]"
Weights of mixture model components
-g,--gamma-rate-heterogeneity "(NCAT,SHAPE)"
Number of gamma rate categories and shape parameter
-l,--length NUMBER Set alignment length to NUMBER
-S,--seed [INT] Seed for random number generator; list of 32 bit
integers with up to 256 elements (default: random)
-h,--help Show this help text
Substitution models:
-s "MODEL[PARAMETER,PARAMETER,...]{STATIONARY_DISTRIBUTION}"
Supported DNA models: JC, F81, HKY, GTR4.
For example,
-s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}
-s GTR4[e_AC,e_AG,e_AT,e_CG,e_CT,e_GT]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}
where the 'e_XY' are the exchangeabilities from nucleotide X to Y.
Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom, GTR20.
MODEL-Custom means that only the exchangeabilities of MODEL are used,
and a custom stationary distribution is provided.
For example,
-s LG
-s LG-Custom{...}
-s GTR20[e_AR,e_AN,...]{...}
the 'e_XY' are the exchangeabilities from amino acid X to Y (alphabetical order).
Notes: The F81 model for DNA is equivalent to the Poisson-Custom for proteins.
The GTR4 model for DNA is equivalent to the GTR20 for proteins.
Mixture models:
-m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2[PARAMETERS]{STATIONARY_DISTRIBUTION},...)"
For example,
-m "MIXTURE(JC,HKY[6.0]{0.3,0.2,0.2,0.3})"
Mixture weights have to be provided with the -w option.
Special mixture models:
-m CXX
where XX is 10, 20, 30, 40, 50, or 60; CXX models, Quang et al., 2008.
-m "EDM(EXCHANGEABILITIES)"
Arbitrary empirical distribution mixture (EDM) models.
Stationary distributions have to be provided with the -e or -p option.
For example,
LG exchangeabilities with stationary distributions given in FILE.
-m "EDM(LG-Custom)" -e FILE
LG exchangeabilities with site profiles (Phylobayes) given in FILES.
-m "EDM(LG-Custom)" -p FILES
For special mixture models, mixture weights are optional.
## Sub-sample
Sub-sample columns from multi sequence alignments.
slynx sub-sample --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE
(-n|--number-of-sites INT)
(-m|--number-of-alignments INT) [-S|--seed [INT]]
Sub-sample columns from multi sequence alignments.
Available options:
-h,--help Show this help text
-V,--version Show version
-a,--alphabet NAME Specify alphabet type NAME
INPUT-FILE Read sequences from INPUT-FILE
-n,--number-of-sites INT Number of sites randomly drawn with replacement
-m,--number-of-alignments INT
Number of multi sequence alignments to be created
-S,--seed [INT] Seed for random number generator; list of 32 bit
integers with up to 256 elements (default: random)
-h,--help Show this help text
Create a given number of multi sequence alignments, each of which contains a given number of random sites drawn from the original multi sequence alignment.
## Translate
Translate sequences.
slynx translate --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)
(-u|--universal-code CODE)
Translate from DNA to Protein or DNAX to ProteinX.
Available options:
-h,--help Show this help text
-V,--version Show version
-a,--alphabet NAME Specify alphabet type NAME
INPUT-FILE Read sequences from INPUT-FILE
-r,--reading-frame INT Reading frame [0|1|2].
-u,--universal-code CODE universal code; one of: Standard,
VertebrateMitochondrial.
-h,--help Show this help text
# TLynx
Handle phylogenetic trees in Newick format.
tlynx --help | head -n -16
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
Compare, examine, and simulate phylogenetic trees.
Available options:
-h,--help Show this help text
-V,--version Show version
-v,--verbosity VALUE Be verbose; one of: Quiet Warning Info
Debug (default: Info)
-o,--output-file-basename NAME
Specify base name of output file
-f,--force Ignore previous analysis and overwrite existing
output files.
--no-elynx-file Do not write files for needed for reproducibility.
Available commands:
compare Compare two phylogenetic trees (compute distances and branch-wise differences).
connect Connect two phylogenetic trees in all ways (possibly honoring constraints).
distance Compute distances between many phylogenetic trees.
examine Compute summary statistics of phylogenetic trees.
shuffle Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves).
simulate Simulate phylogenetic trees using a birth and death or coalescent process.
Available tree file formats:
- Newick Standard: Branch support values are stored in square brackets after branch lengths.
- Newick IqTree: Branch support values are stored as node names after the closing bracket of forests.
- Newick RevBayes: Key-value pairs is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are ignored at the moment.
## Compare
Compute distances between phylogenetic trees.
tlynx compare --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect]
[-f|--newick-format FORMAT] NAMES
Compare two phylogenetic trees (compute distances and branch-wise differences).
Available options:
-h,--help Show this help text
-V,--version Show version
-n,--normalize Normalize trees before comparison
-b,--bipartitions Print and plot common and missing bipartitions
-t,--intersect Compare intersections; i.e., before comparison, drop
leaves that are not present in the other tree
-f,--newick-format FORMAT
Newick tree format: Standard, IqTree, or RevBayes;
default: Standard; for detailed help, see 'tlynx
--help'
NAMES Tree files
-h,--help Show this help text
## Examine
Compute summary statistics of phylogenetic trees.
tlynx examine --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
Compute summary statistics of phylogenetic trees.
Available options:
-h,--help Show this help text
-V,--version Show version
INPUT-FILE Read trees from INPUT-FILE
-f,--newick-format FORMAT
Newick tree format: Standard, IqTree, or RevBayes;
default: Standard; for detailed help, see 'tlynx
--help'
-h,--help Show this help text
## Simulate
Simulate phylogenetic trees using birth and death processes.
tlynx simulate --help
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS
[-u|--sub-sample DOUBLE] [-s|--summary-statistics]
[-S|--seed [INT]]
Simulate phylogenetic trees using a birth and death or coalescent process.
Available options:
-h,--help Show this help text
-V,--version Show version
-t,--nTrees INT Number of trees
-n,--nLeaves INT Number of leaves per tree
-u,--sub-sample DOUBLE Perform sub-sampling; see below.
-s,--summary-statistics For each branch, print length and number of children
-S,--seed [INT] Seed for random number generator; list of 32 bit
integers with up to 256 elements (default: random)
-h,--help Show this help text
Available processes:
birthdeath Birth and death process
coalescent Coalescent process
See, for example, 'tlynx simulate birthdeath --help'.
Sub-sample with probability p:
1. Simulate one big tree with n'=round(n/p), n'>=n, leaves;
2. Randomly sample sub-trees with n leaves.
(With p=1.0, the same tree is reported over and over again.)
# ELynx
Validate and (optionally) redo past ELynx analyses.
elynx --help | head -n -16
ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: elynx COMMAND
Validate and redo past ELynx analyses
Available options:
-h,--help Show this help text
-V,--version Show version
Available commands:
validate Validate an ELynx analysis
redo Redo an ELynx analysis