First task Calculate the time complexity and space complexity for the following Alignment Methods
State the time complexity with prove
Mummer,RTD,kmacs,ACS,Spaced,cvt,Jspecies tetra,Jspecies ANIm,Jspecies ANIb,ANI,Pyani ANIm,Pyani ANIb,Pyani Tetra,Blast,Kmer,Cophylog,Kr,gram
Second Task
1. Get 10 genomes from different species (known taxonomy on NCBI)
2. Average 2 ANI distances between each 2 species
3. Compare all others (Methods) to that
Third Task
obtain the phylogenetic tree using alignment methods. perform all popular alignment techniques, then vote for the most commonly generated tree, this tree can then be used as a reference to compare other methods.
pyani --> [login to view URL]
mummer --> [login to view URL]
blast --> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
kmacs -->[login to view URL]
co-phylog-->[login to view URL]
Co-phylog: a bioinformatics tool for Phylogenetic inference | Phylogenomics
Creates a micro-alignment in a sequence using the context of an object. Co-phylog is a phylogenomic approach that takes advantage of unassembled next-generation sequencing (NGS) data from complete genomes. This application has similar computing efficiency with ‘word frequencies’ based on alignme...
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spaced words -->[login to view URL]
JAN 26TH, 3:03AM
ffp --> [login to view URL]
kmacs -->[login to view URL]
JSpecies not available as source code
CVT -->[login to view URL]
kmer -->[login to view URL]