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QuickTree : Building big trees (quickly)

QuickTree : Building big trees (quickly). Three years old – why talk about it now? About to start releasing a tree flat-file Application note in Bioinformatics Trees in Pfam Tree-order alignments NIFAS Method: Neighbour-joining. while (| L | > 2) {

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QuickTree : Building big trees (quickly)

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  1. QuickTree : Building big trees (quickly) • Three years old – why talk about it now? • About to start releasing a tree flat-file • Application note in Bioinformatics • Trees in Pfam • Tree-order alignments • NIFAS • Method: Neighbour-joining

  2. while (|L| > 2) { 1. Find i, j that minimises Dij = dij – (ri + rj), where 2. Make new node k and set dkm = (dim + djm – dij) / 2, for all m in L 3. Join i and j to k with dik = (dij + ri – rj) / 2 djk = dik – dik 4. Remove i and j from L and add k } Neighbour-joining

  3. 1. Find i, j that minimises Dij = dij – (ri + rj), where for i = 1 to |L| { for j = 1 to |L| {… for k = 1 to |L| {… for k = 1 to |L| {… while(|L| > 2) { for i = 1 to |L| { for j = 1 to |L| Dij = dij – (ri + rj) … } } Make new node Update matrix } Clustal W / Phylip => O(n4)QuickTree => O(n3)

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