Provided by: fasttree_2.1.10-2_amd64 bug

NAME

       fasttree - create phylogenetic trees from alignments of nucleotide or protein sequences

DESCRIPTION

       fasttree  infers  approximately-maximum-likelihood  phylogenetic  trees from alignments of
       nucleotide or protein sequences. It handles alignments with up to a million  of  sequences
       in a reasonable amount of time and memory.

       fasttree  is more accurate than PhyML 3 with default settings, and much more accurate than
       the distance-matrix methods that are traditionally used  for  large  alignments.  fasttree
       uses  the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution
       and the JTT (Jones-Taylor-Thornton 1992) model of amino acid evolution. To account for the
       varying  rates  of  evolution across sites, fasttree uses a single rate for each site (the
       "CAT" approximation). To quickly estimate the reliability  of  each  split  in  the  tree,
       fasttree  computes  local  support values with the Shimodaira-Hasegawa test (these are the
       same as PhyML 3's "SH-like local supports").

SYNOPSIS

       fasttree protein_alignment > tree

       fasttree -nt nucleotide_alignment > tree

       fasttree -nt -gtr < nucleotide_alignment > tree

       fasttree accepts alignments in fasta or phylip interleaved formats

   Common options (must be before the alignment file):
       -quiet to suppress reporting information

       -nopr to suppress progress indicator

       -log logfile -- save intermediate trees, settings, and model details

       -fastest -- speed up the neighbor joining phase & reduce memory usage

              (recommended for >50,000 sequences)

       -n <number> to analyze multiple alignments (phylip format only)

              (use for global bootstrap, with seqboot and CompareToBootstrap.pl)

       -nosupport to not compute support values

       -intree newick_file to set the starting tree(s)

       -intree1 newick_file to use this starting tree for all the alignments

              (for faster global bootstrap on huge alignments)

       -pseudo to use pseudocounts (recommended for highly gapped sequences)

       -gtr -- generalized time-reversible model (nucleotide alignments only)

       -wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)

       -quote -- allow spaces and other restricted characters (but not ' characters) in

              sequence names and quote names in the output tree (fasta input only; fasttree  will
              not be able to read these trees back in

       -noml to turn off maximum-likelihood

       -nome to turn off minimum-evolution NNIs and SPRs

              (recommended if running additional ML NNIs with -intree)

       -nome -mllen with -intree to optimize branch lengths for a fixed topology

       -cat # to specify the number of rate categories of sites (default 20)

              or -nocat to use constant rates

       -gamma -- after optimizing the tree under the CAT approximation,

              rescale the lengths to optimize the Gamma20 likelihood

       -constraints constraintAlignment to constrain the topology search

              constraintAlignment should have 1s or 0s to indicates splits

       -expert -- see more options

   Detailed usage for fasttree 2.1.4 SSE3:
       fasttree [-nt] [-n 100] [-quote] [-pseudo | -pseudo 1.0]

              [-boot    1000    |    -nosupport]    [-intree   starting_trees_file   |   -intree1
              starting_tree_file] [-quiet | -nopr] [-nni 10] [-spr 2] [-noml |  -mllen  |  -mlnni
              10]  [-mlacc  2]  [-cat  20  |  -nocat] [-gamma] [-slow | -fastest] [-2nd | -no2nd]
              [-slownni] [-seed 1253] [-top | -notop] [-topm 1.0 [-close  0.75]  [-refresh  0.8]]
              [-matrix Matrix | -nomatrix] [-nj | -bionj] [-wag] [-nt] [-gtr] [-gtrrates ac ag at
              cg ct gt] [-gtrfreq A C G T] [ -constraints constraintAlignment [ -constraintWeight
              100.0 ] ] [-log logfile]

              [ alignment_file ]

              > newick_tree

       or

       fasttree [-nt] [-matrix Matrix | -nomatrix] [-rawdist] -makematrix [alignment]

              [-n 100] > phylip_distance_matrix

              fasttree  supports  fasta  or  phylip  interleaved  alignments  By default fasttree
              expects protein alignments,  use -nt for nucleotides fasttree reads standard  input
              if no alignment file is given

   Input/output options:
       -n -- read in multiple alignments in. This only

              works  with  phylip interleaved format. For example, you can use it with the output
              from phylip's seqboot. If you use -n, fasttree  will  write  1  tree  per  line  to
              standard output.

       -intree newickfile -- read the starting tree in from newickfile.

              Any branch lengths in the starting trees are ignored.

       -intree with -n will read a separate starting tree for each alignment.

       -intree1 newickfile -- read the same starting tree for each alignment

       -quiet -- do not write to standard error during normal operation (no progress

              indicator, no options summary, no likelihood values, etc.)

       -nopr -- do not write the progress indicator to stderr

       -log logfile -- save intermediate trees so you can extract

              the  trees  and  restart  long-running  jobs  if  they  crash -log also reports the
              per-site rates (1 means slowest category)

       -quote -- quote sequence names in the output and allow spaces, commas,

              parentheses, and colons in them but not ' characters (fasta files only)

   Distances:
              Default: For protein sequences, log-corrected distances and an

              amino acid dissimilarity matrix derived from BLOSUM45

              or for nucleotide sequences, Jukes-Cantor distances To specify a different  matrix,
              use  -matrix FilePrefix or -nomatrix Use -rawdist to turn the log-correction off or
              to use %different instead of Jukes-Cantor

       -pseudo [weight] -- Use pseudocounts to estimate distances between

              sequences with little or no overlap. (Off by default.) Recommended if analyzing the
              alignment has sequences with little or no overlap.  If the weight is not specified,
              it is 1.0

   Topology refinement:
              By default, fasttree tries to improve the tree  with  up  to  4*log2(N)  rounds  of
              minimum-evolution  nearest-neighbor  interchanges  (NNI),  where N is the number of
              unique sequences, 2 rounds of subtree-prune-regraft (SPR) moves (also  min.  evo.),
              and  up  to 2*log(N) rounds of maximum-likelihood NNIs.  Use -nni to set the number
              of rounds of min. evo. NNIs, and -spr to set the rounds of SPRs.  Use -noml to turn
              off both min-evo NNIs and SPRs (useful if refining

              an approximately maximum-likelihood tree with further NNIs)

              Use  -sprlength set the maximum length of a SPR move (default 10) Use -mlnni to set
              the number of rounds of maximum-likelihood NNIs Use -mlacc 2 or -mlacc 3 to  always
              optimize all 5 branches at each NNI,

              and to optimize all 5 branches in 2 or 3 rounds

              Use -mllen to optimize branch lengths without ML NNIs Use -mllen -nome with -intree
              to optimize branch lengths on a fixed topology Use -slownni to turn off  heuristics
              to avoid constant subtrees (affects both

              ML and ME NNIs)

   Maximum likelihood model options:
       -wag -- Whelan-And-Goldman 2001 model instead of (default) Jones-Taylor-Thorton 1992 model
              (a.a. only)

       -gtr -- generalized time-reversible instead of (default) Jukes-Cantor (nt only)

       -cat # -- specify the number of rate categories of sites (default 20)

       -nocat -- no CAT model (just 1 category)

       -gamma -- after the final round of optimizing branch lengths with the CAT model,

              report the likelihood under the discrete  gamma  model  with  the  same  number  of
              categories.  fasttree  uses  the  same branch lengths but optimizes the gamma shape
              parameter and the scale of the lengths.  The final tree will have rescaled lengths.
              Used  with  -log, this also generates per-site likelihoods for use with CONSEL, see
              GammaLogToPaup.pl and documentation on the fasttree web site.

   Support value options:
              By  default,  fasttree  computes  local  support  values  by  resampling  the  site
              likelihoods  1,000 times and the Shimodaira Hasegawa test. If you specify -nome, it
              will compute minimum-evolution bootstrap  supports  instead  In  either  case,  the
              support values are proportions ranging from 0 to 1

              Use  -nosupport  to  turn off support values or -boot 100 to use just 100 resamples
              Use -seed to initialize the random number generator

   Searching for the best join:
              By default, fasttree combines the 'visible set' of fast neighbor-joining with

              local hill-climbing as in relaxed neighbor-joining

       -slow -- exhaustive search (like NJ or BIONJ, but different gap handling)

       -slow takes half an hour instead of 8 seconds for 1,250 proteins

       -fastest -- search the visible set (the top hit for each node) only

              Unlike the  original  fast  neighbor-joining,  -fastest  updates  visible(C)  after
              joining  A  and  B  if  join(AB,C)  is better than join(C,visible(C)) -fastest also
              updates out-distances in a very lazy way,  -fastest  sets  -2nd  on  as  well,  use
              -fastest -no2nd to avoid this

   Top-hit heuristics:
              By  default,  fasttree uses a top-hit list to speed up search Use -notop (or -slow)
              to turn this feature off

              and compare all leaves to each other, and all new joined nodes to each other

       -topm 1.0 -- set the top-hit list size to parameter*sqrt(N)

              fasttree estimates the top m hits of a leaf from the top  2*m  hits  of  a  'close'
              neighbor,  where  close  is  defined  as d(seed,close) < 0.75 * d(seed, hit of rank
              2*m), and updates the top-hits as joins proceed

       -close 0.75 -- modify the close heuristic, lower is more conservative

       -refresh 0.8 -- compare a joined node to all other nodes if its

              top-hit list is less than 80% of the desired length, or if the age of  the  top-hit
              list is log2(m) or greater

       -2nd or -no2nd to turn 2nd-level top hits heuristic on or off

              This  reduces  memory usage and running time but may lead to marginal reductions in
              tree quality.  (By default, -fastest turns on -2nd.)

   Join options:
       -nj: regular (unweighted) neighbor-joining (default)

       -bionj: weighted joins as in BIONJ

              fasttree will also weight joins during NNIs

   Constrained topology search options:
       -constraints alignmentfile -- an alignment with values of 0, 1, and -

              Not all sequences need be present. A column of 0s  and  1s  defines  a  constrained
              split.  Some  constraints may be violated (see 'violating constraints:' in standard
              error).

       -constraintWeight -- how strongly to weight the constraints. A value of 1

              means a penalty of 1 in tree length for violating a constraint Default: 100.0

       For more information, see http://www.microbesonline.org/fasttree/

              or the comments in the source code

              fasttree protein_alignment > tree fasttree -nt nucleotide_alignment > tree fasttree
              -nt -gtr < nucleotide_alignment > tree

       fasttree accepts alignments in fasta or phylip interleaved formats

   Common options (must be before the alignment file):
       -quiet to suppress reporting information

       -nopr to suppress progress indicator

       -log logfile -- save intermediate trees, settings, and model details

       -fastest -- speed up the neighbor joining phase & reduce memory usage

              (recommended for >50,000 sequences)

       -n <number> to analyze multiple alignments (phylip format only)

              (use for global bootstrap, with seqboot and CompareToBootstrap.pl)

       -nosupport to not compute support values

       -intree newick_file to set the starting tree(s)

       -intree1 newick_file to use this starting tree for all the alignments

              (for faster global bootstrap on huge alignments)

       -pseudo to use pseudocounts (recommended for highly gapped sequences)

       -gtr -- generalized time-reversible model (nucleotide alignments only)

       -wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)

       -quote -- allow spaces and other restricted characters (but not ' characters) in

              sequence  names and quote names in the output tree (fasta input only; fasttree will
              not be able to read these trees back in

       -noml to turn off maximum-likelihood

       -nome to turn off minimum-evolution NNIs and SPRs

              (recommended if running additional ML NNIs with -intree)

       -nome -mllen with -intree to optimize branch lengths for a fixed topology

       -cat # to specify the number of rate categories of sites (default 20)

              or -nocat to use constant rates

       -gamma -- after optimizing the tree under the CAT approximation,

              rescale the lengths to optimize the Gamma20 likelihood

       -constraints constraintAlignment to constrain the topology search

              constraintAlignment should have 1s or 0s to indicates splits

       -expert -- see more options

       For more information, see http://www.microbesonline.org/fasttree/