{{ 432star.nex | star.nex }}\\ {{ 432xmastree.lhs | xmastree.lhs }}\\ 



====== Phylogenetic tree with christmassy organisms ======


===== Sequences =====

|**Organism**|**URL to NCBI**|
|Rangifer tarandus (reindeer)|[[http://www.ncbi.nlm.nih.gov/nuccore/DQ318375.1?report=fasta|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|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|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|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|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|http://www.ncbi.nlm.nih.gov/nuccore/L37582.1?report=fasta]]|

===== Processing =====
All programs can be called from [[http://mobyle.pasteur.fr/|http://mobyle.pasteur.fr/]] 


  - Rename  labels in FASTA file to short, appropriate names 
  - 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); 



<file>          +-Abies_alba
          +---1 
  +-------2   +-Euphorbia_pulcherrima
  !       ! 
  !       +---Rangifer_tarandus
  ! 
  ! +Bos_taurus
  3-4 
  ! +---Homo_sapiens
  ! 
  +--Cyprinus_carpio</file>
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|

===== Marger genes =====


<file>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</file>