Index of /EvidentialGene/arthropods/nasoniawasp/orthology

 Name                              Last modified       Size  

 Parent Directory                  25-Mar-2019 14:24      -  
 arp11u11-orthomcl-count.tab       26-Jan-2012 10:46   688k  
 arp11u11-orthomcl-groupsum.txt    29-Jan-2012 19:05     2k  
 arp11u11.clusters.newick          28-Jan-2012 17:56  1008k  
 arp11u11.clusters.tab             28-Jan-2012 22:05   177k  
 arp11u11_genes.ugp.txt.gz         26-Jan-2012 10:56   2.6M  
 arp11u11_genes.ugp.xml.gz         28-Jan-2012 22:06   3.1M  
 arp11u11_genes.ugp_hym.txt        26-Jan-2012 10:56   5.3M  
 arp11u11_omcl11.commongroup.gids  26-Jan-2012 10:57   1.1M  
 arp11u11_omcl11.commongroup.oids  26-Jan-2012 10:57    30k  
 arp11u11_omclgn.consensus_def.txt 26-Jan-2012 10:56   1.2M  
 arp11u11noalt.aa.gz               25-Jan-2012 14:03  53.3M  
 gbtsa_hym_micdemol/               14-Nov-2012 15:55      -  
 gvenn/                            29-Nov-2011 16:58      -  
 phyl/                             30-Jan-2012 15:40      -  
 tables/                           19-May-2012 18:26      -

Hymenoptera-Arthropod Orthomcl gene group summary
2012/January (ARP9, version arp11u11)

            Gene Groups         Genes  Unique-spp Orthologous  Proportions
        nGroup  OrGrp OrMis1    nGene Uniq1  UDup Orth1 OrDup  pDup  pOne
antc      9614   9329    116    15133  3378  1342  8751  1662   0.6   1.2
anth      9633   9291    107    15029  2943  1567  8710  1809   0.7   1.2
apis      8591   8560    170    10145   987    88  8182   888   0.2   0.9
bombi     8971   8962     56     9869   454    20  8674   721   0.1   0.9
bombt     8629   8619    138     9492   430    21  8334   707   0.1   0.9
wasp     10293   8983     92    24296  5446  6686  8239  3925   2.1   1.4

drosmel   8464   7636    187    14289  2824  2556  6994  1915   0.9   1.0
tribol    8893   8388    116    16985  4586  2163  7608  2628   1.0   1.2
aphid    10042   7479    377    38440  7045 13926  5524 11945   5.2   1.3
daphnia   9399   7249    486    30506  7736 12314  6345  4111   3.3   1.4
human     8190   6902    891    20238  3752  5491  4657  6338   2.4   0.8
#---------------------------------------------------------------------------
Notes:
antc, anth = Camponotus and Harpegnathos ants; apis = Apis mellifera;
bombi, bombt = Bombus impatiens, terrestris bumble bees
apis, bombi, bombt are from Ncbi refseq, deficient in duplicates and unique singletons by protocol
wasp = Nasonia vitripennis genes from evigene.pub11u.good set

nGroup  = number of gene family groups (2+genes), orthology + species-unique
OrGrp   = count of ortho groups (nGroup = OrGrp + unique paralog groups)
Uniq1   = species-unique single gene
UDup    = species-unique duplicated paralog genes
Orth1   = count of single ortho gene
OrDup   = count of duplicated ortho gene
OrMis1  = groups missing gene all others have (ignoring human)
pDup, pOne = proportion duplicated, singleton genes relative to median insect d:5000, s:10000
#---------------------------------------------------------------------------

arp11u11: Common gene families presense, ncommon=8147, min taxa=6
Species Have    Miss
wasp    7772    375
antc    7718    429
anth    7703    444
bombi   7666    481
apis    7515    632
bombt   7481    666
tribol  7153    994
drosmel 6803    1344
aphid   6388    1759
daphnia 6156    1991
human   5925    2222

Developed at the Genome Informatics Lab of Indiana University Biology Department