# The ELynx Suite Version: 0.6.1.1. Reproducible evolution made easy.

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 Up to date ELynx Suite version 0.6.1.1. Developed by Dominik Schrempf. Compiled on February 22, 2022, at 15:10 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 Up to date ELynx Suite version 0.6.1.1. Developed by Dominik Schrempf. Compiled on February 22, 2022, at 15:10 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.