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
what do we look for?
max parsimony and the tree that maximises likelihood
what has sequence evolution done?
found rates of replacement of each nuclei
rates define the probabilities of all events over all times
likelihood vs parsimony?
likelihood most accurate
parsimony doesn’t use all available info
advantage - allows well established stat methods
dis - computational cost
what is bootstrapping?
sampling characteristics by randomly choosing vertical columns from aligned sequences to produce a new sequence alignment of same length
why is bootstrapping used?
used to generate pool of plausible trees in max likelihood
simple way to acertain clade support
majority-rule consensus tree
