Version 2.1.11: May 17, 2019

	Added the -trans option to read a transition matrix (and
	stationary distribution) from a file. This is for amino acid
	alignments only.

Version 2.1.10: April 11, 2017

	Fix a bug when using GTR models with huge alignments with over 2
	billion non-gap characters. The frequencies of A, C, G, and T were
	being computed with a 32-bit (signed) counter. This led to
	negative frequencies and eventually to a crash with
	"FastTree.c:9769: tqli: Assertion `iter < 30' failed.". SetMLGtr()
	now uses 64-bit counters. Also, more information about the
	optimization of the GTR model is saved in the log file (if using
	the -log option). To support this, gtr_opt_t now includes fpLog.

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
