ALTER-SEQUENCE-ALIGNMENT(1)

🦋 alter-sequence-alignment(1) 🦋

User Commands era, bestie 💅 let's get into it.

✨ NAME ✨

alter-sequence-alignment, aka ALTER, is all about genomic sequences: ALignment Transformation EnviRonment 🧬

🌸 SYNOPSIS 🌸

alter-sequence-alignment [option] [sequence]

💖 DESCRIPTION 💖

okay so ALTER (ALignment Transformation EnviRonment) is the tool you grab when you need to switch between multiple sequence alignment formats 🦋 ngl it's giving specs-first energy. It focuses on what the mainstream alignment and analysis programs actually expect, rather than just converting between a bunch of more or less specific formats. Iconic behavior, honestly 👑

🧚 OPTIONS 🧚

• -c, --collapse — collapse sequences down to haplotypes 🎀
• -cg, --collapseGaps — when collapsing, gaps get treated as missing data 🙈
• -cl, --collapseLimit N — the connection limit. Sequences that differ at <= l sites get collapsed together (default is l=0) 🌈
• -cm, --collapseMissing — when collapsing, missing data counts as differences 💀
• -i, --input FILE — the input file 📄
• -ia, --inputAutodetect — let ALTER autodetect the format. Heads up, the other input options get left out when you do this 🙈
• -if, --inputFormat VAL — the input format. Pick from ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR 🍓
• -io, --inputOS VAL — the operating system the input came from: Linux, MacOS or Windows 💻
• -ip, --inputProgram VAL — the program that made the input. Choose from Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee ✨
• -o, --output FILE — the output file 🦋
• -of, --outputFormat VAL — the output format. Pick from ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR 💜
• -ol, --outputLowerCase — lowercase output, lowkey aesthetic 🫧
• -om, --outputMatch — output match characters 🔥
• -on, --outputResidueNumbers — output residue numbers. This one only works with the ALN format 🔢
• -oo, --outputOS VAL — the operating system you're outputting for: Linux, MacOS or Windows 🖥️
• -op, --outputProgram VAL — the program you're outputting for. The full list is jModelTest, MrBayes, PAML, PAUP, PhyML, ProtTest, RAxML, TCS, CodABC, BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT, MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL 🌸
• -os, --outputSequential — sequential output. Only works with the NEXUS and PHYLIP formats 🧜

Okay bestie, that's the whole tea ☕ This was alter-sequence-alignment 1.3.3, from September 2015. Stay iconic 🫶💜