The ELynx Suite
Version: 0.2.2.
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 four library packages and three executables providing
a range of sub commands.
The library packages are:
- 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.
-
Install Stack with your package manager, or directly from the web
page.
curl -sSL https://get.haskellstack.org/ | sh
-
Clone the ELynx repository.
git clone clone https://github.com/dschrempf/elynx
-
Navigate to the newly created elynx folder and build the binaries.
This will take a while.
stack build
-
Run a binary from within the project directory. For example,
stack exec tlynx -- --help
-
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.
SLynx
Handle evolutionary sequences.
slynx --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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)
- 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 sub commands:
slynx examine --help
Concatenate
Concatenate multi sequence alignments.
slynx concatenate --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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
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 sub commands:
slynx examine --help
Examine
Examine sequence with slynx examine.
slynx examine --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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
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 sub commands:
slynx examine --help
Filter
Filter sequences with filer-rows.
slynx filter-rows --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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
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 sub commands:
slynx examine --help
Filter columns of multi sequence alignments with filter-columns.
slynx filter-columns --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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
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 sub commands:
slynx examine --help
Simulate
Simulate sequences with slynx simulate.
slynx simulate --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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 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.
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 sub commands:
slynx examine --help
Sub-sample
Sub-sample columns from multi sequence alignments.
slynx sub-sample --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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.
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 sub commands:
slynx examine --help
Translate
Translate sequences.
slynx translate --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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
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 sub commands:
slynx examine --help
TLynx
Handle phylogenetic trees in Newick format.
tlynx --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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.
- 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.
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 sub commands:
slynx examine --help
Compare
Compute distances between phylogenetic trees.
tlynx compare --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 pm, UTC.
Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect]
[-f|--newick-format FORMAT] NAME
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; see 'tlynx
--help' (default: Standard)
NAME Tree file
-h,--help Show this help text
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 sub commands:
slynx examine --help
Examine
Compute summary statistics of phylogenetic trees.
tlynx examine --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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; see 'tlynx
--help' (default: Standard)
-h,--help Show this help text
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 sub commands:
slynx examine --help
Simulate
Simulate phylogenetic trees using birth and death processes.
tlynx simulate --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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
-----
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 sub commands:
slynx examine --help
ELynx
Validate and (optionally) redo past ELynx analyses.
elynx --help
ELynx Suite version 0.2.1.
Developed by Dominik Schrempf.
Compiled on April 27, 2020, at 12:08 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
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 sub commands:
slynx examine --help
Library documentation
Documentation of the libraries can be found on Hackage:
Documentation of the executables is also available:
