fasttreeMP(1)

🌳 fasttreeMP(1) — User Commands 💅

okay bestie, sit DOWN, because fasttreeMP is about to become your whole personality 🦋 (it's the openMP version, iykyk)

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✨ NAME ✨

fasttreeMP — create phylogenetic trees from alignments of nucleotide or protein sequences (openMP version) 🌈

🌸 DESCRIPTION 🌸

So basically, fasttreeMP infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. And when I say it handles a lot?? It handles alignments with up to a million sequences in a reasonable amount of time and memory. A MILLION. no cap.

And the accuracy?? fasttreeMP 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. it's giving main character energy honestly 👑

Here's the tea on the models it uses:

• for nucleotide evolution: the Jukes-Cantor or generalized time-reversible (GTR) models
• for amino acid evolution: the JTT (Jones-Taylor-Thornton 1992) model

And to account for the varying rates of evolution across sites, fasttreeMP uses a single rate for each site (the "CAT" approximation) 🐱

To quickly estimate the reliability of each split in the tree, fasttreeMP computes local support values with the Shimodaira-Hasegawa test — and these are literally the same as PhyML 3's "SH-like local supports" 💖 periodt.

📜 SYNOPSIS 📜

fasttreeMP protein_alignment > tree

fasttreeMP -nt nucleotide_alignment > tree

fasttreeMP -nt -gtr < nucleotide_alignment > tree

fasttreeMP accepts alignments in fasta or phylip interleaved formats ✨

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🎀 Common options (must be before the alignment file)

bestie. BEFORE the alignment file. I'm not playing. 🙈

• -quiet — to suppress reporting information
• -nopr — to suppress the 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; fasttreeMP 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 👀

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🔥 Detailed usage for fasttreeMP 2.1.4 SSE3 🔥

fasttreeMP [-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

fasttreeMP [-nt] [-matrix Matrix | -nomatrix] [-rawdist] -makematrix [alignment]
       [-n 100] > phylip_distance_matrix

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

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📥 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, fasttreeMP 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)

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🧮 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

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🌿 Topology refinement

By default, fasttreeMP 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)

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🧬 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. fasttreeMP 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 fasttreeMP web site.

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🫶 Support value options

By default, fasttreeMP 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

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🔍 Searching for the best join

By default, fasttreeMP 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.

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🎯 Top-hit heuristics

By default, fasttreeMP 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)

fasttreeMP 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.)

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🔗 Join options

• -nj — regular (unweighted) neighbor-joining (default)
• -bionj — weighted joins as in BIONJ

fasttreeMP will also weight joins during NNIs

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🚧 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

…and to finish that thought, bestie: it 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.

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

fasttreeMP accepts alignments in fasta or phylip interleaved formats.

✨ Common options (must be before the alignment file) ✨

• -quiet — suppresses reporting information. It's giving silent treatment 💅
• -nopr — suppresses the progress indicator. No little spinner, just vibes ✨
• -log logfile — saves intermediate trees, settings, and model details to logfile. Keep the receipts 🧾
• -fastest — speeds up the neighbor joining phase & reduces memory usage. Recommended for >50,000 sequences. Big alignment? This is the move 🔥
• -n <number> — analyzes multiple alignments (phylip format only). Use for global bootstrap, with seqboot and CompareToBootstrap.pl.
• -nosupport — does not compute support values. No support, no problem 💁‍♀️
• -intree newick_file — sets the starting tree(s). Starting point slay 🌱
• -intree1 newick_file — uses this starting tree for all the alignments (for faster global bootstrap on huge alignments). One tree to rule them all 👑
• -pseudo — uses pseudocounts (recommended for highly gapped sequences). Gap girlies, this one's for you 🫶
• -gtr — generalized time-reversible model (nucleotide alignments only). Nucleotide besties only 🧬
• -wag — Whelan-And-Goldman 2001 model (amino acid alignments only). Protein besties only 🧪
• -quote — allows spaces and other restricted characters (but not ' characters) in sequence names and quote names in the output tree (fasta input only; fasttreeMP will not be able to read these trees back in). So quoted names, but don't try to reread them, no cap 💀
• -noml — turns off maximum-likelihood. ML? Not today 💅
• -nome — turns off minimum-evolution NNIs and SPRs (recommended if running additional ML NNIs with -intree).
• -nome -mllen with -intree — optimizes branch lengths for a fixed topology.
• -cat # — specifies the number of rate categories of sites (default 20). Or -nocat — uses constant rates.
• -gamma — after optimizing the tree under the CAT approximation, rescales the lengths to optimize the Gamma20 likelihood.
• -constraints constraintAlignment — constrains the topology search. constraintAlignment should have 1s or 0s to indicates splits.
• -expert — see more options. Expert mode unlocked 🔓

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

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This page is from Lawrence Berkeley National Lab, dated June 2012, and it's for fasttreeMP(1). Bye bestie, go build some trees 🌳💖