Version 2.1.9: March 29, 2016
Add the -lg option to use Le/Gascuel model for amino acid
substitutions. (Thanks to Doug Phelan and Ashley Superson at
Oakland University.)
Version 2.1.8: March 24, 2015
To provide useful branch lengths for very wide alignments of very
close closely-related sequences, the minimum branch lengths were
dramatically decreased when compiling with USE_DOUBLE. If using ML
on an alignment of closely-related and long sequences, issues a
warning, and recommends recompiling with USE_DOUBLE (if not
already using USE_DOUBLE).
Version 2.1.7: January 22, 2013
To avoid numerical problems that led to crashes in rare cases,
increased the minimum branch length for likelihood optimization
from 1e-4 to 5e-4.
Also added a compile-time option to use double-precision instead
of single-precision floating point (compile with
-DUSE_DOUBLE). This allowed verification that single-precision
floating point does not reduce the accuracy of topologies on
simulations with 5,000-78,000 sequences. Also, if accurate shorter
branch lengths are needed (i.e. for analyzing a very wide
alignment or very similar sequences), then double-precision should
allow a significant reduction in the branch length constants
MLMinBranchLength and MLMinRelBranchLength.
Version 2.1.6: September 20, 2012
Corrected a segmentation fault while computing support values for
alignments with over 1 million positions. This arose due to
allocating an array with #boostraps * #positions integers: for
huge alignments, the size of this array would overflow 32-bit
arithmetic.
Version 2.1.5: August 30, 2012
Added the -out option to meet popular demand
Added a warning for Windows users to run it inside a command shell
Version 2.1.4: July 28, 2011
Added the -quote option (thanks to Samuel Shepard at the CDC)
Added the -wag option (thanks to Siavash Mirarab at UT Austin)
Version 2.1.3: April 12, 2010
Corrected a bug that could lead to infinite recursion and stack
overflow within the NJ phase with -fastest
Version 2.1.2: March 24, 2010
Corrected a bug with printing out trees when sequence names
contain the "%" character.
Version 2.1.1: December 12, 2009
Corrected a numerical problem that caused earlier versions to
crash on highly gappy protein alignments: added gapFreq to
distance_matrix_t and use it in NormalizeFreq if we have a
virtually-all-gap profile position.
Version 2.1.0: October 15, 2009
Implemented fast Gamma20 log likelihoods (-gamma). By default,
FastTree reports CAT-based log likelihoods, which are not
necessarily comparable across runs or to likelihoods from other
tools. With the -gamma option, FastTree can now report a
likelihood under the "Gamma20" model, which accounts for rate
variation across sites with a discrete gamma distribution with 20
categories. FastTree computes this likelihood without
reoptimizing the branch lengths under the new model -- instead, it
optimizes a scale factor for all branch lengths and the shape
parameter of the gamma distribution. Nevertheless, for large
trees, these likelihoods should be very accurate. The Gamma20
likelihoods are quite fast to compute: for alignments with >= 500
sequences, -gamma should slow FastTree down by at most 5%. With
-gamma, FastTree also reports more accurate branch lengths.
Added reporting of per-site likelihoods (under -gamma -log) and
the accessory script GammaLogToPaup.pl to convert this for use by
CONSEL.
Rewrote the top-hits code to use 8 rather than 20 bytes per entry
in the top-hits lists and to be faster. Leads to slight changes in
results but not to any consistent change in tree quality, even
without NNIs or SPRs.
Other reductions in memory usage: (1) reallocate posterior
distributions to ensure that we save space (realloc was not
shrinking them effectively). (2) Eliminate the 2nd copy of the
alignment.
With -fastest, added a 2nd level of top-hits heuristic to reduce
memory usage and running time for the neighbor joining phase. Let
q = sqrt(m) = N**0.25. FastTree will store top-hits lists of size
q for the top q hits of any gene that has a 1st-level top-hits
list, and will go back to the seed to get more candidate hits
instead of doing a full refresh when these "2nd-level" lists
become too short. FastTree will also create top-hits lists for the
top q/2 hits of any seed, even if it fails the close check. Does
not affect accuracy in huge simulations, but may lead to slight
reductions in tree quality. Use -fastest -no2nd to turn off
2nd-level top-hits.
Added the OpenMP version. Most steps are parallelized: key
exceptions are ML lengths, optimizing rate categoriess, ME NNIs
and ME SPRs. The parallelizing of the ML phase only uses 3
threads. With OpenMP, the top-hits phase becomes non-deterministic
and the star topology test is turned off.
Version 2.0.1: August 26, 2009
Add a work-around for numerical problems in Jukes-Cantor model on
huge alignments (see "replaced weight %f with %f")
Report scaling of CAT model's rate categories to stderr (unless
-quiet is used)
Version 2.0.0: July 22, 2009
Accounted for variable rates across sites with the CAT
approximation to the gamma model used by RAxML (see A. Stamitakis,
"Phylogenetic models of rate heterogeneity: a high performance
computing perspective", IPDPS 2006). The site categories are set
once, after the first round of NNIs or (if using -mllen) after the
first round of optimizing branch lengths. FastTree uses a Bayesian
approach to avoid overfitting these rates.
Implemented SH-like local supports, as in PhyML 3. In practice,
FastTree's supports are nearly identical to those from PhyML with
the discrete Gamma-4 model, despite the CAT approximation. One
difference is that FastTree reports 0 for a "bad split" that turns
out to support a different topology, instead of reporting the
(negative) likelihood difference as the support value. During this
phase, FastTree also reports any "bad" splits (NNIs that would
improve the likelihood) and whether these are due to constraints
or not.
Implemented the generalized time-reversible nucleotide model of
evolution (-gtr option). The base frequencies are the same as in
the alignment; the rates are optimized just before selecting site
categories. Or use -gtrfreq and -gtrrates to set them yourself.
Improvements to heuristics for maximum-likelihood NNIs:
(1) Fixed a bug in the code for deciding whether to skip the 2nd
round of optimizing branch lengths around a quartet.
(2) Skip the 2nd round if one of the NNIs is a clear winner, not
just if the original topology is a clear winner.
(3) Skip the 2nd round if we are allowing the star test, the
original topology is winning, and the internal branch lengths of
the alternatives are roughly 0, as a biologically significant
improvement is unlikely.
(4) Skip traversing into an entire subtree if no significant
improvement in that subtree has been found in either of the last
two rounds. This affects minimum-evolution NNIs as well. Use
-slownni to turn off subtree skipping.
(5) This allows us to increase the default number of rounds of
minimum-evolution NNIs to 4*log2(N) and the default number of
rounds of maximum-likelihood NNIs to 2*log2(N)..
(6) Stop doing NNIs if no significant tree improvements were found
in the last round.
(7) But, add a single slow round of ML NNIs at the end to catch
the rare errors that result from all the heuristics.
The -mllen option, in combination with -intree and -nome, lets you
optimize branch lengths for a fixed topology.
The -log option saves intermediate trees, settings, and model
details to the specified log file.
Use SSE3 instructions if the compiler has set __SSE__ to indicate
that they are available. SSE3 improves performance of protein
maximum likelihood up to 50% and speeds up the protein
minimum-evolution code slightly. Nucleotide code may be slightly
faster or slightly slower. Use -DNO_SSE to compile without SSE
instructions.
Sped up convergence in the branch length optimizer by tweaking the
selection of starting bounds for the brent method and by
terminating optimization if the new guess differs by less than
0.2% of the length or less than 0.0001.
Reduce posterior profile computations while optimizing a quartet
from 10 to 7 (AB, CD, ABC, ABD, CD with new branch lengths, ACD,
BCD).
Raised default -constraintWeight to 100 because 10 is not that big
a difference in log likelihoods.
Use exact posteriors for protein sequences by default.
Version 1.9.0: June 19, 2009
Added maximum-likelihood nearest-neighbor interchanges, with the
Jukes-Cantor model for nucleotide data or the Jones-Taylor-Thorton
model for amino acid data, and no variation in rates across sites.
By default, do O(log N) rounds of maximum-likelihood NNIs, but
quit if the total tree log-likelihood has converged (it improves
by less than 0.1 over the last round).
When considering NNI moves (3 possible quartets), FastTree
optimizes all 5 branch lengths in turn, up to a branch length
accuracy of 0.001. By default it uses two rounds of optimizing the
5 branch lengths to estimate the log-likelihood for the
quartet. During the first round of NNIs, the minimum-evolution
profiles and branch lengths are used initially, but they are
gradually replaced by the posterior distributions and the
maximum-likelihood branch lengths.
Two heuristics to speed up ML NNIs: the star topology test and the
one-round heuristic.
Star topology test: If ((A,B),(C,D)) is noticeably more likely
than the star topology (the log-likelihood with the optimal
internal branch length is at least 5 better), and there was no NNI
at this node or its neighbors in the previous round, then do not
optimize the other branch lengths or estimate log likelihoods for
` the other topologies.
One-round heuristic: If after the 1st round of optimizing 5 branch
lengths for the 3 possible quartet topologies, the log-likelihood
value is more than 5 worse than the original topology, do not
optimize that topology further (no 2nd round of optimizing branch
lengths).
For amino acid data, uses an eigen-representation of posterior
distributions at internal nodes to compute likelihoods in O(a)
time, not O(a***2) time, where a is the alphabet size. However,
computing posterior distributions still takes O(a**2) time. Uses
an approximation to reduce this to O(a) time if the posterior
distribution is dominated by one amino acid and the approximation
is accurate.
For the Jukes-Cantor model, the posterior distribution of a
character and a gap, or of two characters that match (potentially
also mixed with gaps or uncertainty) is the same as another
character mixed with a gap. FastTree uses this representation to
save memory and CPU time.
Added many command-line options relating to maximum-likelihood
NNIs, such as -mlnni to change the maxinum number of rounds of ML
NNIs, -mlacc 2 to turn off the ML heuristics (or higher values to
optimize the branch lengths for a quartet of posterior profiles
more thoroughly), -mlexact to turn off approximate posteriors,
-noml to turn off ML computations entirely, and -nome to turn off
minimum-evolution computations entirely (except that
minimum-evolution is still used to get initial branch lengths).
change the number of rounds of ML NNIs.)
Make sure profiles are updated on the way "back up" during NNIs
Version 1.1.0: May 11, 2009
Added heuristic subtree-prune-regraft moves. As suggested by
Richard Desper and Olivier Gascuel, each SPR is treated as a chain
of NNIs, and FastTree uses the sum of changes in lengths of
internal branches as an estimate of the change in tree length for
the SPR. (In FastME's balanced NNIs, the change in internal branch
length is the same as the change in tree length, but for FastTree,
this is an approximation because of the log-of-averages
vs. averages-of-logs issue.) By default, FastTree does two rounds
of SPRs, with exhaustive search for moves up to length two. Then
it extends each of these moves up to a length of 10 along the best
step at each point. (You can use -spr 0 to turn these off, as they
are a bit slow and only seem to improve accuracy slightly.)
Doubled the default number of rounds of NNIs.
Switch to using balanced joins by default, as they are much faster
and have no apparent impact on accuracy.
Tweaked the top-hits heuristic to be more aggressive -- the
default -close value is now log(N)/(log(N)+2). This makes it
noticeably faster on huge alignments, without any impact on
accuracy.
Removed O(N**2) steps -- use a sqrt(N) "top-visible" list to
select a candidate for the best join in O(sqrt(N)) time instead of
O(N) time per join. Also update the total profile from scratch much
less frequently.
Use stale out-distances more aggressively, and rescale them by the
number of active nodes. (The intuition behind this optimization is
that the average out-distance changes very little after a join if
we have 1,000 active nodes.)
Optimized the constrained topology search to be faster. The
constraintWeight is now rather ad hoc, but in practice, a weight
of 10 means the constraints are always satisfied.
Warn if appear to be analyzing a protein alignment with -nt or a
nucleotide alignment without -nt
More compact help
Compact reporting of unexpected characters
Progress indicator (unless running with -quiet)
Version 1.0.5: April 8, 2009
Added -intree and -intree1 options to specify a starting tree
before doing NNIs and/or local bootstrap.
Corrected a bug in estimating how many rounds of NNIs to do if
analyzing multiple alignments with the -n option (#NNIs was being
set only from the first alignment's size)
Version 1.0.4: February 4, 2009
Corrected a bug in the local bootstrap that led to overly low
support values for splits that are surrounded by very
closely-related sequences (distances of 0.01 or less).
Version 1.0.3: January 7, 2009
Added constrained topology search
Version 1.0.2: December 15, 2008
Add the -pseudo option
Version 1.0.1: October 27, 2008
Report the total length of the tree (unless using -quiet).
Improvements to the documentation (if you run it with -help) and
to the comments, especially the long comment at the beginning of
the code.
Comment out malloc.h, unless using TRACK_MEMORY, so that it
compiles on Macs.
Version 1.0.0: September 3, 2008
Added nearest-neighbor interchanges (NNIs) according to a
minimum-evolution criterion. This is done in a similar way as in
FastME, but FastTree uses profiles to speed the computation and
uses weighted joins (inspired by BIONJ) to compute profiles of
internal nodes. This change gives significant improvements in the
accuracy of FastTree, partly because the NNIs are beneficial and
partly because FastTree corrects distances for multiple
substitutions (e.g., uses Jukes-Cantor or Poisson-corrected
distances) when doing NNIs but not during the initial
neighbor-joining phase.
Optimized the implementation of local bootstrap and replaced the
probabilistic local supports, which do not transfer well to
log-corrected distances, with the local bootstrap.
Eliminated crashes on alignments with large numbers of
highly-gapped and non-overlapping sequences, by adding checks to
avoid divide-by-zero errors.
Version 0.9.1: April 22, 2008
Fixed bug that crashed windows version if using top-hits
heuristic. Fixing this bug also leads to (rare) changes to
results under Linux.
Allow lower-case letters in input alignments.
Version 0.9: Initial release, April 15, 2008