> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # Alignment Gap Gini > Gap-distribution Gini for pairwise protein alignments (MAFFT); low is even, high is truncated.
Alignment Gap Gini
**License:** MAFFT is open source and free for academic and commercial use under a BSD-3-Clause license. Please refer to [the license](https://mafft.cbrc.jp/alignment/software/license.txt) for full terms.

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evo-design/proto-language/proto\_language/constraint/sequence\_alignment/gap\_gini\_constraint.py
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```bibtex theme={null} @article{katoh2013mafft, title={MAFFT multiple sequence alignment software version 7: improvements in performance and usability}, author={Katoh, Kazutaka and Standley, Daron M}, journal={Molecular Biology and Evolution}, volume={30}, number={4}, pages={772--780}, year={2013}, publisher={Oxford University Press}, doi={10.1093/molbev/mst010} } ```
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Score pairwise protein alignments by gap-distribution Gini coefficient. For each (query, reference) pair the function: 1. Aligns the two protein sequences with MAFFT. 2. Optionally trims (center-crop 80%, strip end gaps). 3. Computes gap run-length Gini for both sequences; takes the max. 4. Returns 0.0 if gap\_gini \<= max\_gap\_gini, else scales linearly to 1.0. ## API Reference
ConfigGapGiniConfig Source
Configuration for the alignment gap Gini constraint. The Gini coefficient measures inequality in the distribution of gap run-lengths within a pairwise alignment. A value near 0 means gaps are evenly distributed; a value near 1 means they are concentrated in a single run (truncation artifact). Maximum acceptable gap Gini score (0-1). Alignments above this are penalized. Center-crop to 80% and strip end gaps before computing the Gini coefficient.
ReturnsConstraintOutput
One result per pair. `score` is 0.0 if the gap distribution is acceptable, up to 1.0 for the worst violation. The `metadata` carries `gap_gini` (and `gap_gini_error` on failure).
## Usage ```python python icon="python" theme={null} from proto_language.core import Constraint from proto_language.constraint import gap_gini_constraint, GapGiniConfig constraint = Constraint( inputs=[segment], function=gap_gini_constraint, function_config=GapGiniConfig( # Configure parameters here ), ) scores = constraint.evaluate() ``` ## Metadata | Property | Value | | --------------- | --------------------- | | Key | `gap-gini` | | Function | `gap_gini_constraint` | | Category | `sequence_alignment` | | Mode | `discrete` | | Uses GPU | `False` | | Supported Types | `protein` |