Phylogenetic Reconstruction Flashcards
what do phylogenetic trees show?
evolutionary relationships among a group of organisms
what are sequence alignments?
the comparison of two or more DNA or protein sequences to each other - used to highlight similarity between sequences
what is alignment?
the procedure of writing two or more sequences in a way that maximises the indentical/similar characters placing in the same column by adding gap characters
what is FASTA?
the standard input format for alignment programs
x used for ambigous characters
how does FASTA output work?
gaps are represented by -
the order of sequences may be different in input and output
move sequences along until parts match up and give the bits that don’t match up a -
gaps score -1, matches 1
what is a gap penalty?
gaps tend to occur together so we use affine costs to make extending an already existing gap cheaper
costs more to open a gap than it does to extend one
what is multiple sequence alignment?
a grid of residues and gaps
what happens if theres residues in the same row?
theyre from the same sequence
what do residues in the same columns share?
some equivalence/similarity
what is progressive alignment?
construct multiple alignments by adding sequences in tree - circular
what is muscle iterative alignment?
the initial guide tree - its cheap but inaccurate
its a fast way of recalculating distances especially with large numbers of sequence/alignments
what is insertion bias?
when an insertion is penalised multiple times - and penalised more than deletion
what are some problems with alignments?
we can’t trust gappy regions
its just a good guess - some better than others
whats maximum parsiomony?
when the tree is scored on the minimum number of evolutionary changes it implies
we look for the most parsimous tree - the one that implies the smallest number of changes - all depends where organisms are placed
what is likelihood?
the probability of data, the biased type is our max likelihood estimate
