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xmastree.lhs

Phylogenetic tree with christmassy organisms

Sequences

OrganismURL to NCBI
Rangifer tarandus (reindeer)http://www.ncbi.nlm.nih.gov/nuccore/DQ318375.1?report=fasta
Cyprinus carpio (carp)http://www.ncbi.nlm.nih.gov/nuccore/FJ710826.1?report=fasta
Bos taurus (ox)http://www.ncbi.nlm.nih.gov/nuccore/NR_036642.1?report=fasta
Abies alba (fir)http://www.ncbi.nlm.nih.gov/nuccore/DQ371809.1?report=fasta
Visum album (Mistletoe)http://www.ncbi.nlm.nih.gov/nuccore/L24426.1?report=fasta
Euphorbia pulcherrima (Poinsettia)http://www.ncbi.nlm.nih.gov/nuccore/L37582.1?report=fasta

Processing

All programs can be called from http://mobyle.pasteur.fr/

  1. Rename labels in FASTA file to short, appropriate names
  2. Perform multiple alignment using clustalw-multialign
    • - make sure to specify PHYLIP as output format 
  Run **dnadist** 
  * - maybe use Jukes-Cantor distance correction 
  Run **neighbor** to obtain a phylogenetic tree 
  Display tree using the inbuilt functionality, or [[http://lh3lh3.users.sourceforge.net/jstree.shtml|http://lh3lh3.users.sourceforge.net/jstree.shtml]] or [[http://iubio.bio.indiana.edu/treeapp/treeprint-form.html|http://iubio.bio.indiana.edu/treeapp/treeprint-form.html]] or whatever you like

Output

(((Abies_alba:0.03384,Euphorbia_pulcherrima:0.03536):0.06867,Rangifer_tarandus:0.08134):0.12522, (Bos_taurus:0.01825,Homo_sapiens:0.07370):0.02523,Cyprinus_carpio:0.04433); 

          +-Abies_alba
          +---1 
  +-------2   +-Euphorbia_pulcherrima
  !       ! 
  !       +---Rangifer_tarandus
  ! 
  ! +Bos_taurus
  3-4 
  ! +---Homo_sapiens
  ! 
  +--Cyprinus_carpio

remember: this is an unrooted tree!

BetweenAndLength
320.12522
210.06867
1Abies_alba0.03384
1Euphorbia_pulcherrima0.03536
2Rangifer_tarandus0.08134
340.02523
4Bos_taurus0.01825
4Homo_sapiens0.07370
3Cyprinus_carpio0.04433

Marger genes

Your sequence should contain at least one of the genes below, which we consider reliable phylogenetic markers:

(the list is shown in the order in which these genes usually occur on the genome)

#1: COG0048 Ribosomal protein S12
#2: COG0049 Ribosomal protein S7
#3: COG0080 Ribosomal protein L11
#4: COG0081 Ribosomal protein L1
#5: COG0087 Ribosomal protein L3
#6: COG0091 Ribosomal protein L22
#7: COG0092 Ribosomal protein S3
#8: COG0197 Ribosomal protein L16/L10E
#9: COG0186 Ribosomal protein S17
#10: COG0093 Ribosomal protein L14
#11: COG0094 Ribosomal protein L5
#12: COG0096 Ribosomal protein S8
#13: COG0097 Ribosomal protein L6P/L9E
#14: COG0256 Ribosomal protein L18
#15: COG0098 Ribosomal protein S5
#16: COG0200 Ribosomal protein L15
#17: COG0201 Preprotein translocase subunit SecY
#18: COG0099 Ribosomal protein S13
#19: COG0100 Ribosomal protein S11
#20: COG0522 Ribosomal protein S4 and related proteins
#21: COG0202 DNA-directed RNA polymerase, alpha subunit/40 kD subunit
#22: COG0102 Ribosomal protein L13
#23: COG0052 Ribosomal protein S2
#24: COG0172 Seryl-tRNA synthetase
#25: COG0495 Leucyl-tRNA synthetase
#26: COG0012 Predicted GTPase, probable translation factor
#27: COG0016 Phenylalanyl-tRNA synthetase alpha subunit
#28: COG0103 Ribosomal protein S9
#29: COG0184 Ribosomal protein S15P/S13E
#30: COG0533 Metal-dependent proteases with possible chaperone activity
#31: COG0525 Valyl-tRNA synthetase