# The ELynx Suite Version: 0.0.1. Reproducible evolution made easy. The ELynx Suite is a Haskell library and a tool set for computational biology. The goal of the ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic trees can be read, viewed, modified and simulated. Exact specification of all options is necessary, and nothing is assumed about the data (e.g., the type of code). The command line with all arguments is consistently, and automatically logged. The work overhead in the beginning usually pays off in the end. The Elynx Suite consists of three library packages and two executables providing a range of sub commands. The library packages are: - **elynx-seq:** Handle evolutionary sequences and multi sequence alignments; - **elynx-tree:** Handle phylogenetic trees; - **elynx-tools:** Tools for the provided executables; The executables are: - **SLynx:** Analyze, modify, and simulate evolutionary sequences (FASTA format); - **TLynx:** Analyze, modify, and simulate phylogenetic trees (Newick format). **ELynx is still under development. We happily receive comments, ideas, feature requests, or 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 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 [PATH](https://en.wikipedia.org/wiki/PATH_(variable)). Then, they can be used directly. # SLynx Handle evolutionary sequences. slynx --help ELynx Suite version 0.5.1. Developed by Dominik Schrempf. Compiled on September 9, 2019, at 10:48 am, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 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 Available commands: concatenate examine If data is a multi sequence alignment, additionally analyze columns. filter-rows filter-columns simulate sub-sample Create a given number of multi sequence alignments, each of which containing a given number of random sites drawn from the original multi sequence alignment. translate File formats: - FASTA Alphabet types: - 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) The ELynx Suite. A Haskell library and a tool set for computational biology. The goal of the ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic trees can be read, viewed, modified and simulated. Exact specification of all options is necessary, and nothing is assumed about the data (e.g., the type of code). The command line with all arguments is consistently, and automatically logged. The work overhead in the beginning usually pays off in the end. slynx Analyze, modify, and simulate evolutionary sequences. tlynx Analyze, modify, and simulate phylogenetic trees. ## Concatenate Concatenate multi sequence alignments. slynx concatenate --help Concatenate sequences found in input files. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Available options: -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 Examine sequences. Usage: slynx examine (-a|--alphabet NAME) [INPUT-FILE] [--per-site] If data is a multi sequence alignment, additionally analyze columns. Available options: -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 Filter rows (or sequences) found in input files. Usage: slynx filter-rows (-a|--alphabet NAME) [INPUT-FILE] [--longer-than LENGTH] [--shorter-than LENGTH] Available options: -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 -h,--help Show this help text Filter columns of multi sequence alignments with `filter-columns`. slynx filter-columns --help Filter columns of multi-sequence alignments. Usage: slynx filter-columns (-a|--alphabet NAME) [INPUT-FILE] [--standard-chars DOUBLE] Available options: -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 Simulate multi sequence alignments. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"] [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"] (-l|--length NUMBER) [-S|--seed [INT]] Available options: -t,--tree-file Name Read trees from 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 -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, HKY. For example, -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE} Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom. MODEL-Custom means that only the exchangeabilities of MODEL are used, and a custom stationary distribution is provided. For example, -s LG-Custom{...} Mixture models: -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2)" 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 option. For example, LG exchangeabilities with stationary distributions given in FILE. -m "EDM(LG-Custom)" -e FILE For special mixture models, mixture weights are optional. ## Sub-sample Sub-sample columns from multi sequence alignments. slynx sub-sample --help Usage: slynx sub-sample (-a|--alphabet NAME) [INPUT-FILE] (-n|--number-of-sites INT) (-m|--number-of-alignments INT) [-S|--seed [INT]] Create a given number of multi sequence alignments, each of which containing a given number of random sites drawn from the original multi sequence alignment. Available options: -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 ## Translate Translate sequences. slynx translate --help Translate from DNA to Protein or DNAX to ProteinX. Usage: slynx translate (-a|--alphabet NAME) [INPUT-FILE] (-r|--reading-frame INT) (-u|--universal-code CODE) Available options: -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 ELynx Suite version 0.5.1. Developed by Dominik Schrempf. Compiled on September 9, 2019, at 10:48 am, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 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 Available commands: compare examine simulate Simulate reconstructed trees using the point process. See Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005 File formats: - Newick The ELynx Suite. A Haskell library and a tool set for computational biology. The goal of the ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic trees can be read, viewed, modified and simulated. Exact specification of all options is necessary, and nothing is assumed about the data (e.g., the type of code). The command line with all arguments is consistently, and automatically logged. The work overhead in the beginning usually pays off in the end. slynx Analyze, modify, and simulate evolutionary sequences. tlynx Analyze, modify, and simulate phylogenetic trees. ## Compare Compute distances between phylogenetic trees. tlynx compare --help Compute distances between phylogenetic trees. Usage: tlynx compare (-d|--distance MEASURE) [-s|--summary-statistics] [INPUT-FILES] Available options: -d,--distance MEASURE Type of distance to calculate (available distance measures are listed below) -s,--summary-statistics Report summary statistics only INPUT-FILES Read tree(s) from INPUT-FILES; if more files are given, one tree is expected per file -h,--help Show this help text Available distance measures: Symmetric distance: -d symmetric Incompatible split distance: -d incompatible-split[VAL] Collapse branches with support less than VAL before distance calculation; in this way, only well supported difference contribute to the distance measure. ## Examine Compute summary statistics of phylogenetic trees. tlynx examine --help Compute summary statistics of phylogenetic trees. Usage: tlynx examine [INPUT-FILE] Available options: INPUT-FILE Read trees from INPUT-FILE -h,--help Show this help text ## Simulate Simulate phylogenetic trees using birth and death processes. tlynx simulate --help Simulate phylogenetic trees using birth and death processes. Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] [-M|--condition-on-mrca] [-l|--lambda DOUBLE] [-m|--mu DOUBLE] [-r|--rho DOUBLE] [-u|--sub-sample] [-s|--summary-statistics] [-S|--seed [INT]] Simulate reconstructed trees using the point process. See Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005 Available options: -t,--nTrees INT Number of trees (default: 10) -n,--nLeaves INT Number of leaves per tree (default: 5) -H,--height DOUBLE Fix tree height (no default) -M,--condition-on-mrca Do not condition on height of origin but on height of MRCA -l,--lambda DOUBLE Birth rate lambda (default: 1.0) -m,--mu DOUBLE Death rate mu (default: 0.9) -r,--rho DOUBLE Sampling probability rho (default: 1.0) -u,--sub-sample Perform sub-sampling; see below. -s,--summary-statistics Only output number of children for each branch -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 Height of Trees: if no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate. Summary statistics only: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character. Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again. # ELynx Documentation of the library can be found on Hackage.