domains / families / science / alignment-trimming

alignment-trimming

separate

Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

When to use

• removing unreliable columns
• removing contaminating residues
• phylogenetic inference preparation
• HMM building preparation
• selection analysis preparation
• filtering columns based on gap fraction
• filtering columns based on conservation
• filtering columns based on entropy

When not to use

• sequence-level outlier filtering
• aggressive trimming for deep-divergence orthologs
• column trimming for single short genes

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