esl-shuffle

name	esl-shuffle
description	Use when shuffling biological sequences, bootstrapping alignment columns, or generating de novo random RNA, DNA, or protein controls.
disable-model-invocation	true
user-invocable	true

esl-shuffle

Quick Start

• Command: esl-shuffle [options] <seqfile> (shuffle sequences)
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-shuffle
• Help: See references/help.md for full options (access with -h)

When To Use This Tool

• Use esl-shuffle when you need randomized controls derived from existing sequences or alignments.
• Default mode shuffles individual sequences; -A switches to multiple-alignment shuffling; -G generates de novo random sequences.
• Reach for -d, -0, -1, -w, or -r when you want a specific preservation model for sequence-based controls.
• Use -b or -v in -A mode for bootstrap-like or per-column randomized alignment controls.

Common Patterns