Analysis Description -------------------- GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc tests run to distinguish topological incongruence from rate-variation. v0.2 adds and spooling results to JSON after each breakpoint search conclusion - __Requirements__: A sequence alignment. - __Citation__: **Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901 - __Written by__: Sergei L Kosakovsky Pond - __Contact Information__: spond@temple.edu - __Analysis Version__: 0.2 type: nucleotide rv: None >Maximum number of breakpoints to consider (permissible range = [1,100000], default value = 10000, integer): max-breakpoints: 10000 mode: Faster >Loaded a nucleotide multiple sequence alignment with **11** sequences, **4008** sites (981 of which are variable) from `/home/datamonkey/datamonkey-js-server/production/app/gard/output/65d89322f17fd757eef458e9` >Minimum size of a partition is set to be 19 sites ### Fitting the baseline (single-partition; no breakpoints) model * Log(L) = -14597.25, AIC-c = 29248.89 (27 estimated parameters) ### Performing an exhaustive single breakpoint analysis Done with single breakpoint analysis. Best single break point location: 1671 c-AIC = 28862.29946619031 ### Performing multi breakpoint analysis using a genetic algorithm Done with 2 breakpoint analysis. Best break point locations: 880, 1671 c-AIC = 28564.48255034238 Done with 3 breakpoint analysis. Best break point locations: 101, 880, 1657 c-AIC = 28431.32119591709 Done with 4 breakpoint analysis. Best break point locations: 95, 880, 1670, 3429 c-AIC = 28320.23409615293 Done with 5 breakpoint analysis. Best break point locations: 95, 882, 1694, 3430, 3684 c-AIC = 28231.72966012037 Done with 6 breakpoint analysis. Best break point locations: 96, 882, 1478, 1682, 3410, 3677 c-AIC = 28161.64746233815 Done with 7 breakpoint analysis. Best break point locations: 98, 882, 1604, 1682, 2402, 3410, 3677 c-AIC = 28085.61556554195 Done with 8 breakpoint analysis. Best break point locations: 98, 881, 1604, 1682, 2262, 2390, 3410, 3677 c-AIC = 28029.70014950018 Done with 9 breakpoint analysis. Best break point locations: 105, 883, 1103, 1609, 1697, 2252, 2390, 3410, 3677 c-AIC = 27972.59028236198 Done with 10 breakpoint analysis. Best break point locations: 105, 651, 883, 1103, 1609, 1697, 2252, 2390, 3410, 3677 c-AIC = 27939.20285168341 Done with 11 breakpoint analysis. Best break point locations: 105, 540, 651, 883, 1103, 1609, 1697, 2252, 2390, 3410, 3677 c-AIC = 27851.77184089243 Done with 12 breakpoint analysis. Best break point locations: 105, 540, 651, 827, 883, 1103, 1609, 1697, 2252, 2390, 3410, 3677 c-AIC = 27804.92241078072 Done with 13 breakpoint analysis. Best break point locations: 105, 357, 540, 651, 827, 883, 1103, 1609, 1697, 2252, 2390, 3410, 3677 c-AIC = 27771.82984258608 Done with 14 breakpoint analysis. Best break point locations: 105, 357, 540, 677, 827, 883, 1103, 1517, 1609, 1697, 2252, 2390, 3410, 3677 c-AIC = 27732.74874096047 Done with 15 breakpoint analysis. Best break point locations: 105, 357, 404, 540, 677, 827, 883, 1103, 1517, 1609, 1697, 2252, 2390, 3410, 3677 c-AIC = 27678.58456916631 Done with 16 breakpoint analysis. Best break point locations: 105, 357, 392, 571, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 3410, 3677 c-AIC = 27640.6405152291 Done with 17 breakpoint analysis. Best break point locations: 105, 357, 392, 571, 611, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 3410, 3677 c-AIC = 27629.56103753116 Done with 18 breakpoint analysis. Best break point locations: 105, 357, 392, 545, 571, 611, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 3410, 3677 c-AIC = 27614.83062774098 Done with 19 breakpoint analysis. Best break point locations: 105, 357, 392, 545, 571, 611, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 3410, 3677, 3860 c-AIC = 27585.49883417975 Done with 20 breakpoint analysis. Best break point locations: 105, 357, 392, 545, 571, 611, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 3410, 3555, 3677, 3860 c-AIC = 27565.12576701431 Done with 21 breakpoint analysis. Best break point locations: 105, 357, 392, 545, 571, 611, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 2931, 3410, 3555, 3677, 3860 c-AIC = 27558.06807711151 Done with 22 breakpoint analysis. Best break point locations: 105, 149, 357, 392, 545, 571, 611, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 2931, 3410, 3555, 3677, 3860 c-AIC = 27553.2986525745 Done with 23 breakpoint analysis. Best break point locations: 105, 149, 357, 392, 545, 571, 611, 677, 824, 883, 1103, 1517, 1609, 1697, 2252, 2288, 2390, 2931, 3410, 3555, 3593, 3677, 3860 c-AIC = 27531.96576225455 Done with 24 breakpoint analysis. Best break point locations: 105, 150, 357, 392, 551, 573, 611, 677, 818, 883, 1099, 1517, 1616, 1699, 2249, 2291, 2390, 2660, 3119, 3410, 3555, 3593, 3677, 3857 c-AIC = 27506.88266252246 Done with 25 breakpoint analysis. Best break point locations: 105, 150, 357, 392, 551, 573, 611, 677, 818, 883, 1099, 1517, 1616, 1699, 1994, 2249, 2291, 2390, 2660, 3119, 3410, 3555, 3593, 3677, 3857 c-AIC = 27502.71569525474