Organism | URL 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 |
All programs can be called from http://mobyle.pasteur.fr/
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
(((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!
Between | And | Length |
3 | 2 | 0.12522 |
2 | 1 | 0.06867 |
1 | Abies_alba | 0.03384 |
1 | Euphorbia_pulcherrima | 0.03536 |
2 | Rangifer_tarandus | 0.08134 |
3 | 4 | 0.02523 |
4 | Bos_taurus | 0.01825 |
4 | Homo_sapiens | 0.07370 |
3 | Cyprinus_carpio | 0.04433 |
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