elynx-seq-0.7.2.2: README.md
# The ELynx Suite
Version: 0.7.2.1.
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](https://hackage.haskell.org/package/elynx-nexus):** Nexus file support.
- **[elynx-markov](https://hackage.haskell.org/package/elynx-markov):** Simulate multi sequence alignments along phylogenetic trees.
- **[elynx-seq](https://hackage.haskell.org/package/elynx-seq):** Handle evolutionary sequences and multi sequence alignments.
- **[elynx-tools](https://hackage.haskell.org/package/elynx-tools):** Tools for the provided executables.
- **[elynx-tree](https://hackage.haskell.org/package/elynx-tree):** Handle phylogenetic trees.
The executables are:
- **[slynx](https://hackage.haskell.org/package/slynx):** Analyze, modify, and simulate evolutionary sequences.
- **[tlynx](https://hackage.haskell.org/package/tlynx):** Analyze, modify, and simulate phylogenetic trees.
- **[elynx](https://hackage.haskell.org/package/elynx):** Validate and redo past analyses.
Documentation is available on [Hackage](https://hackage.haskell.org/) (use direct links above).
**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 [cabal-install](https://cabal.readthedocs.io/en/3.4/cabal-commands.html) or [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.
# Get help
cabal run slynx -- --help
# OR: stack exec slynx -- --help
# OR: slynx --help
ELynx Suite version 0.7.2.1.
Developed by Dominik Schrempf.
Compiled on June 15, 2023, at 19:54 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 Warn 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 data required to reproduce an analysis.
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)
- ProteinI (amino acids; including gaps, translation stops, and IUPAC codes)
ELynx
-----
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.
slynx Analyze, modify, and simulate evolutionary sequences.
tlynx Analyze, modify, and simulate phylogenetic trees.
elynx Validate and redo past analyses.
Get help for commands:
slynx --help
Get help for sub commands:
slynx examine --help
## Sub command
The documentation of sub commands can be accessed separately:
cabal run slynx -- simulate --help
# OR: stack exec slynx -- simulate --help
# OR: slynx simulate --help
ELynx Suite version 0.7.2.1.
Developed by Dominik Schrempf.
Compiled on June 15, 2023, at 19:54 pm, UTC.
Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
[-m|--mixture-model MODEL] [-n|--global-normalization]
[-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)
-n,--global-normalization
Normalize mixture model globally (one normalization
constant for all components)
-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 (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.