Rearrangements + parameter estimation
and or or: Grammar or else ...
What dawg has and Rose hasn't:
What iSG has:
What GSIMULATOR/SIMGRAM/SIMGENOME has
What covers the infinite sites model?
The infinite sites model treats chromosomes either as continuous intervals or continuous circles, which are divided in sites. No breakpoints are reused. Model can be transfered to finite sites model with some special characteristics.
Kantenlängen bedeutung: nicht wie bei Rose 1 (Kantenlänge 1 = Mutationswahrscheinlichkeit 1%) use of a Markov-Cain
average sequence length n character frequencies /* UndefinedMacro: latex($f=(f_1,\ldots,f_\ell)$) */
mutation guide tree //**T**// (edge length, standard: 1) * OR
sequence distance /* UndefinedMacro: latex($d_{AV}$) */ (generate binary T over average pairwise sequence distance)
mutation matrix /* UndefinedMacro: latex($M,\ \ \ell\times\ell$) */ (pairwise mutation frequencies for substitutions insertion / deletion probability functions * /* UndefinedMacro: latex($\begin{array}{lclll}p_{ins}&/&p_{del}&&\mbox{probabilities}\\\ell_{ins}&/&\ell_{del}&&\mbox{indel lengths}\end{array}$) */
mutation <del>probability</del> likelihood vector /* UndefinedMacro: latex($\nu,\ \ |\nu|=n$) */ (specify sequence motifs)
Groups as follows:
Input Marvin Rolf Stefan | Tree/Evolution Christoph Eyla Konstantin | Output Marvin Rolf Stefan |
Grammar Daniel Kai Madis |
2 possibilities:
Problems:
Alternative: Markov Models/chains (HMM)
Circular vs. Linear Edge length: discrete vs. continous
Input | Tree | Grammar | Output | Input→Interior |
genomes ? | ||||
root sequence OR length | X | X | root sequence ? | |
annotation | X | X | frequencies, sequences WATCH: copies!! | |
Newick tree OR #species | X | X | Newick tree ? | Roland-Tree |
character frequencies | Transitions | (H)MM | Matrix |
Newick Tree: Roland nach Format fragen & schon fertig geparst übergeben als “Baum-Objekt” - Input - Output - Arbeitsumgebung:
Apart from sequences in the input: Genomes (i.e. linear, circular chromosomes) ?