====== Implementation of Algorithms (1Ü) ======

| 392231 | Stoye, Wittler | Summer 2018 | Class hours by appointment | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=118947240|ekvv]] |

== Final presentation: ==

Tuesday, July 10 at 13:45 in U10-146 or July 16 at 10:00 in U10-146.


== Procedure: ==

Each participant implements a (simple) algorithm in a programming language of their own choice. Topics will be distributed individually: meet or send email to the organizer, a lecturer of any other class or seminar in the modules //Algorithms in Bioinformatics// or //Special Algorithmus in Bioinformatics//. The focus of the implementation shall be on code readability and optimal asymptotics, which ideally is verified by systematic testing.

The source code and some test data (where applicable) has to be sent to the organiser one week before the final presentation. During the final presentation, every participant runs and explains her/his software in front of everybody. If the result is not satisfactory, a correction can be provided until the end of the semester.


== Distributed topics: ==

== Presentation Tuesday, July 10 at 13:45 in U10-146: ==

^ Topic                                     ^ Name                ^ Supervised by  ^
| Neighbor Joining                          | Sarah Becker        | Roland         |
| Agglomerative Clustering                  | Christina Drake     | Roland         |
| Prim's Algorithm                          | Vanessa Krämer      | Roland         |
| Gotoh                                     | Nadine Behrmann     | Roland         |
| Additive tree construction á la Waterman  | Manuel Feser        | Roland         |
| Seller's Algorithm                        | Antonia Leidel      | Roland         |
| Hirschberg                                | Melody Bevan        | Roland         |
| Finding MUMs and MEMs using Suffix Trees  | Timo Wentong Lin    | Roland         |
| BWT incl. backward search                 | Henrike Zimmermann  | Roland         |

== Presentation Monday, July 16 at 10:00 in U10-146: ==

^ Topic                                     ^ Name                ^ Supervised by  ^
| Neighbor Joining                          | Sophia Hönig        | Jens           |
| Agglomerative Clustering                  | Stephanie Wrage     | Jens           |
| Profile Hidden Markov Model Analysis      | Ilja Wolik          | Jens           |
| Perfect Phylogeny                         | Nils Lemke          | Jens           |
| Nussinov-Algorithmus                      | Andreas Rempel      | Jens           |
| The Money Changing Problem                | Ruth Rotgänger      | Jens           |
| <del>Signed Reversal Distance in Linear Time</del> | <del>Tim Rother</del> | <del>Jens</del> |
| Center-Star-Approximation für Multiples Alignment | Duygu Emir  | Jens           |
| Maximal Unique Matches w/ suffix trees | Sophia Hansen | Jens |

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