Phylogenetic Distance Calculator

Phylogenetic distance measures the evolutionary relationship between species based on genetic differences. It quantifies how much two species have diverged from their common ancestor, helping researchers understand evolutionary relationships and timelines.

Jukes-Cantor is suitable for closely related sequences with simple evolutionary models. Kimura 2-Parameter accounts for different transition/transversion rates. Tamura-Nei considers base composition differences. P-distance is the simplest method counting only observed differences.

Pairwise deletion removes gaps for each pair comparison, retaining maximum data. Complete deletion removes all positions with gaps in any sequence. Ignore gaps treats gaps as missing data without affecting distance calculations.

The transition/transversion ratio compares purine-to-purine or pyrimidine-to-pyrimidine changes (transitions) versus purine-to-pyrimidine changes (transversions). Higher ratios indicate more transitions, which are typically more common in evolution.

100-1000 bootstrap replicates provide statistical confidence in distance estimates. More replicates increase accuracy but require more computation time. 100 replicates are usually sufficient for most analyses.

The calculator accepts plain DNA sequences (ATGC) or FASTA format sequences. Remove any headers or formatting and ensure sequences contain only standard nucleotide characters (A, T, G, C, and optionally N for unknown bases).

Accuracy depends on sequence quality, length, and evolutionary model appropriateness. Longer sequences provide more reliable estimates. Consider using multiple methods and comparing results for important analyses.