FastME

FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data.

Forked from https://gite.lirmm.fr/atgc/FastME

Compilation

./configure
make

If compilation succeeds, the binary will be located at src/fastme.

Examples

You can run the examples by

cd examples
../src/fastme -i distances.input.mat
../src/fastme -i nucleic.phy -d4
../src/fastme -i proteic.phy -pL

Troubleshooting

If you do not use automake version 1.18, you may need to re-generate the configure script by

autoreconf --install -force

Usage

See fastme --help

SYNOPSIS
    fastme  [-i input data file]  [-u input user tree file]
    [-o output tree file]  [-O output matrix file]  [-I output information file]
    [-B output bootstrap trees file]  [-a]
    [-m method]  [ -D[model] | -P[model] ]  [-r]  [-e]  [-g[alpha]]  [-n[NNI]]  [-s]  [-w branch]
    [-d datasets]  [-b replicates]  [-z seed]
    [-c]  [-f precision] [-T number of threads]  [-v]  [-V]  [-h] 

    You can use fastme with no arguments, in this case change the value of
    a parameter by typing its corresponding character as shown on screen.

OPTIONS

    -i input data file, --input_data=input data file
        The input data file contains sequence alignment(s)
        or a distance matrix(ces).

    -u input user tree file, --user_tree=input user tree file
        FastME may use an existing topology available in the input user tree file
        which corresponds to the input dataset.

    -o output tree file, --output_tree=output tree file
        FastME will write the infered tree into the output tree file.

    -O output matrix file, --output_matrix=output matrix file
        Use this option if you want FastME to write the distances
        matrix computed from the input alignment in the output matrix file.

    -I output information file, --output_info=output information file
        Use this option if you want FastME to write information
        about its execution in the output information file.

    -B output bootstrap trees file, --output_boot=output bootstrap trees file
        Use this option if you want FastME to write bootstrap trees
        in the bootstrap trees file.

    -a, --append
        Use this option to append results to existing output files (if any).
        By default output files will be overwritten.

    -m method, --method=method
        FastME computes a tree using a distance algorithm.
        You may choose this method from:
        TaxAdd_(B)alME, TaxAdd_(O)LSME, B(I)ONJ (default),
        (N)J or (U)NJ.

    -d[model], --dna=[model]
        Use this option if your input data file contains DNA sequences alignment(s).
        You may also indicate the evolutionary [model] which can be choosen from:
        (p)-distance, R(Y) symmetric, (R)Y, (J)C69, (K)2P, F8(1), F8(4) (default), (T)N93, (L)ogDet.

    -p[model], --protein=[model]
        Use this option if your input data file contains protein sequences alignment(s).
        You may also indicate the evolutionary [model] which can be choosen from:
        (p)-distance, (F)81 like, (L)G (default), (W)AG, (J)TT, Day(h)off, 
        (D)CMut, (C)pRev, (M)tREV, (R)tREV, HIV(b), H(I)Vw or FL(U).

    -r, --remove_gap
        Use this option to completely remove any site which has a gap in
        any sequence. By default, FastME is doing pairwise deletion of gaps.

    -e, --equilibrium
        The equilibrium frequencies for DNA are always estimated by counting
        the occurence of the nucleotides in the input alignment.
        For amino-acid sequences, the equilibrium frequencies are estimated
        using the frequencies defined by the substitution model.
        Use this option if you whish to estimate the amino-acid frequencies
        by counting their occurence in the input alignment.

    -g[alpha], --gamma=[alpha]
        Use this option if you wish to have gamma distributed rates across sites.
        By default, FastME runs with no gamma variation.
        If running FastME with gamma distributed rates across sites, the [alpha] default value is 1.0.
        Only helpful when the input data file contains sequences alignment(s).

    -n[NNI], --nni=[NNI]
        Use this option to do [NNI] tree topology improvement.
        You may choose the [NNI] type from:
        NNI_(B)alME (default) or NNI_(O)LS.

    -s, --spr
        Use this option to do SPR tree topology improvement.

    -w branch, --branch_length=branch
        Use this option to indicate the branch length to assign to the tree.
        You may choose the branch length from: (B)alLS (default), (O)LS
        or (n)one. (n)one is only available with BIONJ, NJ or UNJ.
        Only helpful when not improving the tree topology (no NNI nor SPR).

    -D datasets, --datasets=datasets
        Use this option to indicate the number of datasets in your input
        data file. Default value is 1.

    -b replicates, --bootstrap=replicates
        Use this option to indicate the number of replicates FastME will
        do for bootstrapping. Default value is 0.
        Only helpful when the input data file contains sequences alignment(s).

    -z seed, --seed=seed
        Use this option to initialize randomization with seed value.
        Only helpful when bootstrapping.

    -c
        Use this option if you want FastME only to compute distance matrix.
        Only helpful when the input data file contains sequences alignment(s).

    -f precision, --precision=number of digits after dot
        Use this option to set the number of digits after the dot to use on output.
        Default precision is 12.

    -T number of threads, --nb_threads=number of threads
        Use this option to set the number of threads to use.
        Default number of threads is 4.

    -v value, --verbose=value
        Sets the verbose level to value [0-3].
        Default value is 0.

    -V, --version
        Prints the FastME version.

    -h, --help
        Display this usage.