References$(function(){PrimeFaces.cw("TieredMenu","widget_formSmash_upper_j_idt152",{id:"formSmash:upper:j_idt152",widgetVar:"widget_formSmash_upper_j_idt152",autoDisplay:true,overlay:true,my:"left top",at:"left bottom",trigger:"formSmash:upper:referencesLink",triggerEvent:"click"});}); $(function(){PrimeFaces.cw("OverlayPanel","widget_formSmash_upper_j_idt153_j_idt156",{id:"formSmash:upper:j_idt153:j_idt156",widgetVar:"widget_formSmash_upper_j_idt153_j_idt156",target:"formSmash:upper:j_idt153:permLink",showEffect:"blind",hideEffect:"fade",my:"right top",at:"right bottom",showCloseIcon:true});});

Computational problems in evolution: Multiple alignment, genome rearrangements, and tree reconstructionPrimeFaces.cw("AccordionPanel","widget_formSmash_some",{id:"formSmash:some",widgetVar:"widget_formSmash_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_all",{id:"formSmash:all",widgetVar:"widget_formSmash_all",multiple:true});
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PrimeFaces.cw("AccordionPanel","widget_formSmash_responsibleOrgs",{id:"formSmash:responsibleOrgs",widgetVar:"widget_formSmash_responsibleOrgs",multiple:true}); 2006 (English)Doctoral thesis, comprehensive summary (Other scientific)
##### Abstract [en]

##### Place, publisher, year, edition, pages

Stockholm: KTH , 2006. , iv, 54 p.
##### Series

Trita-CSC-A, ISSN 1653-5723 ; 06/22--SE
##### Keyword [en]

Distance Methods, Tree reconstruction, Sorting by Transpositions, multiple alignment, ancestral sequences
##### National Category

Computer Science
##### Identifiers

URN: urn:nbn:se:kth:diva-4170ISBN: 978-91-7178-511-4OAI: oai:DiVA.org:kth-4170DiVA: diva2:11046
##### Public defence

2007-01-15, FA32, Albanova, Roslagstullsbacken 21, Stockholm, 10:00
##### Opponent

PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt455",{id:"formSmash:j_idt455",widgetVar:"widget_formSmash_j_idt455",multiple:true});
##### Supervisors

PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt461",{id:"formSmash:j_idt461",widgetVar:"widget_formSmash_j_idt461",multiple:true});
#####

PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt467",{id:"formSmash:j_idt467",widgetVar:"widget_formSmash_j_idt467",multiple:true});
##### Note

QC 20110121Available from: 2006-11-15 Created: 2006-11-15 Last updated: 2011-01-21Bibliographically approved
##### List of papers

Reconstructing the evolutionary history of a set of species is a fundamental problem in biology. This thesis concerns computational problems that arise in different settings and stages of phylogenetic tree reconstruction, but also in other contexts. The contributions include:

• A new distance-based tree reconstruction method with optimal reconstruction radius and optimal runtime complexity. Included in the result is a greatly simplified proof that the NJ algorithm also has optimal reconstruction radius. (co-author Jens Lagergren)

• NP-hardness results for the most common variations of Multiple Alignment. In particular, it is shown that SP-score, Star Alignment, and Tree Alignment, are NP hard for all metric symbol distances over all binary or larger alphabets.

• A 1.375-approximation algorithm for Sorting By Transpositions (SBT). SBT is the problem of sorting a permutation using as few block-transpositions as possible. The complexity of this problem is still open and it was a ten-year-old open problem to improve the best known 1.5-approximation ratio. The 1.375-approximation algorithm is based on a new upper bound on the diameter of 3-permutations. Moreover, a new lower bound on the transposition diameter of the symmetric group is presented and the exact transposition diameter of simple permutations is determined. (co-author Tzvika Hartman)

• Approximation, fixed-parameter tractable, and fast heuristic algorithms for two variants of the Ancestral Maximum Likelihood (AML) problem: when the phylogenetic tree is known and when it is unknown. AML is the problem of reconstructing the most likely genetic sequences of extinct ancestors along with the most likely mutation probabilities on the edges, given the phylogenetic tree and sequences at the leafs. (co-author Tamir Tuller)

• An algorithm for computing the number of mutational events between aligned DNA sequences which is several hundred times faster than the famous Phylip packages. Since pairwise distance estimation is a bottleneck in distance-based phylogeny reconstruction, the new algorithm improves the overall running time of many distancebased methods by a factor of several hundred. (co-author Jens Lagergren)

1. Settling the Intractability of Multiple Alignment$(function(){PrimeFaces.cw("OverlayPanel","overlay11041",{id:"formSmash:j_idt503:0:j_idt507",widgetVar:"overlay11041",target:"formSmash:j_idt503:0:partsLink",showEvent:"mousedown",hideEvent:"mousedown",showEffect:"blind",hideEffect:"fade",appendToBody:true});});

2. Fast Neighbor Joining$(function(){PrimeFaces.cw("OverlayPanel","overlay11042",{id:"formSmash:j_idt503:1:j_idt507",widgetVar:"overlay11042",target:"formSmash:j_idt503:1:partsLink",showEvent:"mousedown",hideEvent:"mousedown",showEffect:"blind",hideEffect:"fade",appendToBody:true});});

3. A 1.375-Approximation Algorithm for Sorting by Transpositions$(function(){PrimeFaces.cw("OverlayPanel","overlay11043",{id:"formSmash:j_idt503:2:j_idt507",widgetVar:"overlay11043",target:"formSmash:j_idt503:2:partsLink",showEvent:"mousedown",hideEvent:"mousedown",showEffect:"blind",hideEffect:"fade",appendToBody:true});});

4. Fast Computation of Distance Estimators$(function(){PrimeFaces.cw("OverlayPanel","overlay11044",{id:"formSmash:j_idt503:3:j_idt507",widgetVar:"overlay11044",target:"formSmash:j_idt503:3:partsLink",showEvent:"mousedown",hideEvent:"mousedown",showEffect:"blind",hideEffect:"fade",appendToBody:true});});

5. Reconstruction of Ancestral Genomic Sequences Using Likelihood$(function(){PrimeFaces.cw("OverlayPanel","overlay11045",{id:"formSmash:j_idt503:4:j_idt507",widgetVar:"overlay11045",target:"formSmash:j_idt503:4:partsLink",showEvent:"mousedown",hideEvent:"mousedown",showEffect:"blind",hideEffect:"fade",appendToBody:true});});

References$(function(){PrimeFaces.cw("TieredMenu","widget_formSmash_lower_j_idt1196",{id:"formSmash:lower:j_idt1196",widgetVar:"widget_formSmash_lower_j_idt1196",autoDisplay:true,overlay:true,my:"left top",at:"left bottom",trigger:"formSmash:lower:referencesLink",triggerEvent:"click"});}); $(function(){PrimeFaces.cw("OverlayPanel","widget_formSmash_lower_j_idt1197_j_idt1199",{id:"formSmash:lower:j_idt1197:j_idt1199",widgetVar:"widget_formSmash_lower_j_idt1197_j_idt1199",target:"formSmash:lower:j_idt1197:permLink",showEffect:"blind",hideEffect:"fade",my:"right top",at:"right bottom",showCloseIcon:true});});