University of Arizona, Department of Computer Science

CSc 120: Phylogenetic Trees: Examples

Input file information

The examples below are based on input files of various different sizes. These data files were obtained from the following sources:

Influenza-C: Influenza Research Database, www.fludb.org.
SARS-like bat coronavirus: National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/genomes/SARS/SARS.html
Ebola: National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/nuccore/?term=Ebola

I. Small

These files have a small number of "organisms", each with a "genome sequence" of small length (around 5–10).

tiny00.fasta. 2 "organisms".
tiny01.fasta. 3 "organisms".
tiny02.fasta. 5 "organisms".

II. Medium

Each of these files contains around 8–12 organisms, each with a small portion of its genome (length ∼2000).

Influenza-C-small01.fasta. 8 strains of the Influenza-C virus.
Influenza-C-small02.fasta. 8 strains of the Influenza-C virus.
Influenza-C-small03.fasta. 12 strains of the Influenza-C virus.
Influenza-C-small04.fasta. 9 strains of the Influenza-C virus.

III. Large

These files are larger: either because they have many organisms with partial genomes or because they contain the complete genome sequences of organisms.

Influenza-C.fasta. 37 strains of the Influenza-C virus. Genome sequence lengths range from ∼400 to ∼2300.
Bat-SARSlikeCoV.fasta. 5 strains of a SARS-like coronavirus found in bats. Genome sequence lengths are around 30,000.
Ebola.fasta. 11 strains of the Ebola virus. Genome sequence lengths are around 19,000.

Examples

Note that the pretty-printed outputs shown below are not part of the assignment specification: they are shown simply to illustrate the structure of the trees being computed. The code you submit should not print out the pretty-printed trees.

Input File = tiny01.fasta; N = 3

Output:

((name1, name2), name3)

Pretty-printed tree:

          +--- name1
     +---|
+---|     +--- name2
    |
     +--- name3

Input File = tiny02.fasta; N = 3

Output:

(((name2, name5), name3), (name1, name4))

Pretty-printed tree:

               +--- name2
          +---|
     +---|     +--- name5
    |    |
+---|     +--- name3
    |
    |     +--- name1
     +---|
          +--- name4

Input File = Influenza-C-small01.fasta; N = 6

Output:

((((((gb:AB126191:22-2346, gb:AB126193:22-2151), gb:AB126192:18-2282), gb:AB126194:22-1989), gb:AB126195:30-1727), (gb:AB126196:26-982, gb:AB126196:731-1150)), gb:AB283001:27-888)

Pretty-printed tree:

                              +--- gb:AB126191:22-2346
                         +---|
                    +---|     +--- gb:AB126193:22-2151
               +---|    |
          +---|    |     +--- gb:AB126192:18-2282
         |    |    |
     +---|    |     +--- gb:AB126194:22-1989
+---|    |    |
    |    |     +--- gb:AB126195:30-1727
    |    |
    |    |     +--- gb:AB126196:26-982
    |     +---|
    |          +--- gb:AB126196:731-1150
    |
     +--- gb:AB283001:27-888

Input File = Influenza-C-small04.fasta; N = 6

Output:

(((((gb:KM504280:22-1989, gb:M11638:1-2015), gb:KM504279:22-2151), gb:KM504281:1-1807), gb:KM504282:1-1180), (((gb:LC124979:1-862, gb:M15090:1-894), gb:LC124979:1-741), gb:KM504283:1-935))

Pretty-printed tree:

                         +--- gb:KM504280:22-1989
                    +---|
               +---|     +--- gb:M11638:1-2015
          +---|    |
     +---|    |     +--- gb:KM504279:22-2151
    |    |    |
    |    |     +--- gb:KM504281:1-1807
    |    |
+---|     +--- gb:KM504282:1-1180
    |
    |               +--- gb:LC124979:1-862
    |          +---|
    |     +---|     +--- gb:M15090:1-894
     +---|    |
         |     +--- gb:LC124979:1-741
         |
          +--- gb:KM504283:1-935

Input File = Ebola.fasta; N = 6

Output:

(((((FJ621583.1, FJ621585.1), FJ621584.1), FJ968794.1), ((KC545395.1, KC545396.1), NC_014373.1)), ((KP271018.1, KP271020.1), (KP342330.1, KR824525.1)))

Pretty-printed tree:

                         +--- FJ621583.1
                    +---|
               +---|     +--- FJ621585.1
          +---|    |
         |    |     +--- FJ621584.1
         |    |
     +---|     +--- FJ968794.1
    |    |
    |    |          +--- KC545395.1
    |    |     +---|
+---|     +---|     +--- KC545396.1
    |         |
    |          +--- NC_014373.1
    |
    |          +--- KP271018.1
    |     +---|
    |    |     +--- KP271020.1
     +---|
         |     +--- KP342330.1
          +---|
               +--- KR824525.1