FASTML.SH(1)

🌸 FASTML.SH(1) — bestie's guide to fastml 🌸

okay so this is the manual page for fastml, a User Commands situation, and I am literally so excited to walk you through it. grab a snack, hydrate, and let's get into it 💖

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✨ NAME ✨

fastml — maximum likelihood ancestral amino-acid sequence reconstruction 🦋

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🌈 SYNOPSIS 🌈

fastml [options]

that's it. that's the whole vibe. you just run fastml and hand it options. slay 💅

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🧚 DESCRIPTION 🧚

FastML is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences. no cap, that's the whole thing. 🫶

FastML runs several algorithms that reconstruct the ancestral sequences with emphasis on an accurate reconstruction of both indels and characters. for character reconstruction the previously described FastML algorithms are used to efficiently infer the most likely ancestral sequences for each internal node of the tree. both joint and the marginal reconstructions are provided — you get both, periodt. ✨

for indels reconstruction the sequences are first coded according to the indel events detected within the multiple sequence alignment (MSA) and then a state-of-the-art likelihood model is used to reconstruct ancestral indels states. the results are the most probable sequences, together with posterior probabilities for each character and indel at each sequence position for each internal node of the tree. 😭 iconic honestly.

FastML is generic and is applicable for any type of molecular sequences (nucleotide, protein, or codon sequences). versatility queen 👑

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💅 OPTIONS 💅

• -h — help. bestie. ask for help. it's free 🙈
• -s — sequence input file (for example use -s emySequences/eseq.txt)
• -t — tree input file (if tree is not given, a neighbor joining tree is computed).
• -g — Assume among site rate variation model (Gamma) [By default the program will assume an homogeneous model. very fast, but less accurate!]
• -m — model name
• -mj — [JTT]
• -ml — LG
• -mr — mtREV (for mitochondrial genomes)
• -md — DAY
• -mw — WAG
• -mc — cpREV (for chloroplasts genomes)
• -ma — Jukes and Cantor (JC) for amino acids
• -mn — Jukes and Cantor (JC) for nucleotides
• -mh — HKY Model for nucleotides
• -mg — nucgtr Model for nucleotides
• -mt — tamura92 Model for nucleotides
• -my — yang M5 codons model
• -me — empirical codon matrix

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🎀 Controling the output options 🎀

(controling, yes, with the little spelling quirk, we love her for it 💖)

• -x — tree file output in Newick format [tree.newick.txt]
• -y — tree file output in ANCESTOR format [tree.ancestor.txt]
• -j — joint sequences output file [seq.joint.txt]
• -k — marginal sequences output file [seq.marginal.txt]
• -d — joint probabilities output file [prob.joint.txt]
• -e — marginal probabilities output file [prob.marginal.txt]
• -q — ancestral sequences output format. (-qc = [CLUSTAL], -qf = FASTA, -qm = MOLPHY, -qs = MASE, -qp = PHLIYP, -qn = Nexus)

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👑 Advanced options 👑

• -a — Threshold for computing again marginal probabilities [0.9]
• -b — Do not optimize branch lengths on starting tree [by default branches and alpha are ML optimized from the data]
• -c — number of discrete Gamma categories for the gamma distribution [8]
• -f — don't compute Joint reconstruction (good if the branch and bound algorithm takes too much time, and the goal is to compute the marginal reconstruction with Gamma).
• -z — The bound used. -zs = bound based on sum. -zm based on max. -zb [both]
• -p — user alpha parameter of the gamma distribution [if alpha is not given, alpha and branches will be evaluated from the data (override -b)

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⚠️ heads up bestie: when -g is off, the default is an homogeneous model — very fast, but less accurate! and if you pass -p, it overrides -b. read the brackets, they're doing the heavy lifting fr fr 💀

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and that's the whole page, bestie!! go reconstruct some ancestors, you're gonna eat 🍓

💖 this has been fastml.sh version 3.1, from November 2015 — thank you for coming to my ted talk, mwah 💖