fasttree(1)

🦋 fasttree 🦋

okay bestie, this is the fasttree(1) page 💖 It lives in the User Commands section, so it's a command you run straight from your terminal 💅

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🌸 NAME 🌸

fasttree is all about creating phylogenetic trees from alignments of nucleotide or protein sequences 🌳✨

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💖 DESCRIPTION 💖

okay so fasttree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences 🌸 It can handle alignments with up to a million sequences in a reasonable amount of time and memory, which is literally iconic 👑

it's more accurate than PhyML 3 with default settings ✨ and much more accurate than the distance-matrix methods people traditionally reach for with big alignments 💅

for models, 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 🫶 rates of evolution vary from site to site, so to handle that it uses a single rate for each site (the "CAT" approximation) 🦋 and to quickly estimate how reliable each split in the tree is, it computes local support values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local supports") 🔥

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🌳 SYNOPSIS 🌳

here's how you actually call it 🫶

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): 💅

these ones have to come before the alignment file, bestie 🙈

• -quiet — shh, stop reporting information 🤫
• -nopr — no progress indicator for you 🙅‍♀️
• -log logfile — save intermediate trees, settings, and model details 📝
• -fastest — speeds up the neighbor joining phase and reduces memory usage 🚀 (recommended for >50,000 sequences)
• -n <number> — analyze multiple alignments (phylip format only) 🦋 (use this for global bootstrap, with seqboot and CompareToBootstrap.pl)
• -nosupport — don't compute support values
• -intree newick_file — set the starting tree(s) 🌱
• -intree1 newick_file — use this starting tree for all the alignments 🌈 (for faster global bootstrap on huge alignments)
• -pseudo — 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 — turn off maximum-likelihood 🙅‍♀️
• -nome — turn off minimum-evolution NNIs and SPRs 🙅‍♀️ (recommended if running additional ML NNIs with -intree)
• -nome -mllen — with -intree, optimize branch lengths for a fixed topology 🧚
• -cat # — specify the number of rate categories of sites (default 20) 🌈 or use -nocat to use constant rates
• -gamma — after optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood ✨
• -constraints constraintAlignment — constrain the topology search 🔒 constraintAlignment should have 1s or 0s to indicate splits
• -expert — see more options 👀

🧠 Detailed usage for fasttree 2.1.4 SSE3: 🧠

this is the full, unfiltered usage line for version 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, so use -nt for nucleotides. If no alignment file is given, fasttree reads standard input 🫧

📥 Input/output options: 📥

• -n — read in multiple alignments. 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) — reads 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, you get log-corrected distances and an amino acid dissimilarity matrix derived from BLOSUM45. For nucleotide sequences, you get 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.) This is recommended if your 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 ✨ plus 2 rounds of subtree-prune-regraft (SPR) moves (also min. evo.), and up to 2*log(N) rounds of maximum-likelihood NNIs 🔥

• -nni — sets the number of rounds of min. evo. NNIs 🔁
• -spr — sets the number of rounds of SPRs 🔁
• -noml — turns off both min-evo NNIs and SPRs (useful if refining an approximately maximum-likelihood tree with further NNIs) 🙅‍♀️
• -sprlength — sets the maximum length of a SPR move (default 10) 🪄
• -mlnni — sets the number of rounds of maximum-likelihood NNIs 🔁
• -mlacc 2 or -mlacc 3 — always optimize all 5 branches at each NNI, and optimize all 5 branches in 2 or 3 rounds 💅
• -mllen — optimize branch lengths without ML NNIs 📏
• -mllen -nome (with -intree) — optimize branch lengths on a fixed topology 🧚
• -slownni — turns off heuristics to avoid constant subtrees (affects both ML and ME NNIs) 🙈

⏭️ part 2 picks up with the maximum likelihood model options, so stay tuned 👀🫶

Okay bestie, here's the deets on where to find more 💖 Check out http://www.microbesonline.org/fasttree/ or just read the comments in the source code 🫶

Here's how you actually run it, it's so easy 🧚

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

FastTree takes alignments in fasta or phylip interleaved format, no cap 🌸

Common options (must be before the alignment file)

Okay these options have to go BEFORE the alignment file, so don't mess up the order bestie 🙈

• -quiet — shush the reporting info 🤫 (suppresses the reporting information)
• -nopr — turns off the progress indicator so it stops nagging you 📊
• -log logfile — saves intermediate trees, settings, and model details to your logfile 📝
• -fastest — speeds up the neighbor joining phase and cuts down on memory usage ⚡ (recommended for >50,000 sequences, that's a LOT of sequences 💀)
• -n <number> — analyzes multiple alignments, but ONLY in phylip format 🧩 (use this for global bootstrap, with seqboot and CompareToBootstrap.pl)
• -nosupport — skips computing support values 🙅
• -intree newick_file — sets the starting tree(s) 🌳
• -intree1 newick_file — uses this one starting tree for ALL the alignments 👑 (great for a faster global bootstrap on huge alignments)
• -pseudo — turns on 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 — lets sequence names have spaces and other restricted characters (but not ' characters) and quotes the names in the output tree 🎀 (fasta input only; fasttree will not be able to read these trees back in ⚠️)
• -noml — turns off maximum-likelihood 🙃
• -nome — turns off minimum-evolution NNIs and SPRs 💅 (recommended if you're running additional ML NNIs with -intree)
• -nome -mllen — used with -intree, optimizes branch lengths for a fixed topology 🌿
• -cat # — sets the number of rate categories of sites 🦋 (default 20)
• -nocat — uses constant rates instead 🍓
• -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 indicate splits)
• -expert — unlocks even more options 🧠

Heads up, bestie: trees made with -quote can't be read back in by fasttree, so plan accordingly 🙈

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

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Page brought to you by the Lawrence Berkeley National Lab, June 2012 🍓💖 Stay iconic, bestie 🦋✨