The ELynx Suite

Version: 0.3.1. 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: 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 and can be installed with Stack.

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 environment variable. Then, they can be used directly.

Documentation

Documentation is available on Hackage.

Libraries:

• elynx-nexus
• elynx-markov
• elynx-seq
• elynx-tools
• elynx-tree

Executables:

• elynx
• slynx
• tlynx

SLynx

Handle evolutionary sequences.

slynx --help | head -n -16

ELynx Suite version 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 pm, UTC.

Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
             [-f|--force] 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.

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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 pm, UTC.

Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
             [-f|--force] 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.

Available commands:
  coalesce                 Simulate phylogenetic trees using the coalescent processes (see also the 'simulate' command for simulations using the birth and death process).
  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 birth and death processes (see also the 'coalesce' command for simulations using the 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.

Compare

Compute distances between phylogenetic trees.

tlynx compare --help

ELynx Suite version 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 pm, UTC.

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 phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process).

Available options:
  -h,--help                Show this help text
  -V,--version             Show version
  -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.
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

ELynx

Validate and (optionally) redo past ELynx analyses.

elynx --help | head -n -16

ELynx Suite version 0.3.1.
Developed by Dominik Schrempf.
Compiled on August 3, 2020, at 12:12 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