What do we mean with "model" organisms:

Hundreds of species have had their genome sequenced. As a result, ENSEMBL and BLAST can return an overwhelming number of sequences that are homologs of your query. To avoid cluttering, and to speed things up, CCD² will initially only display sequences belonging to certain species. These species have been selected with two criteria:

1. Their genomes are of high quality
2. They are widely distributed on the phylogenetic tree to avoid oversampling certain branches

Not all species are represented in each alignment, since ENSEMBL analyses each Kingdom separately (except for Animals, which are split into Vertebrates and Invertebrates). As a result, if your query is a plant sequence, only Plant homologs wil be returned, even though there might be homologs in e.g. Fungi.
Also, we try to return at least 10 homologs for each alignment. If not enough homologs from "model" species are present in the results, we will add random sequence from "non-model" species (i.e. the rest of the alignment) to reach the total of 10 homologs.

Representative species:

Vertebrates

Danio rerio (Zebrafish)
Oryzias latipes (Medaka fish)
Xenopus laevis, (African clawed frog)
Mus musculus (Mouse)
Homo sapiens (You)
Gallus gallus (Chicken)
Anolis carolinensis (Carolina anole lizard)
Meleagris gallopavo (Turkey)
Sarcophilus harrisii (Tasmanian devil)

Invertebrates

Brugia malayi (Nematoda)
Daphnia pulex (Crustacea)
Strigamia maritima (Myriapoda)
Tribolium castaneum (Coleoptera)
Aedes aegypti (Diptera)
Drosophila melanogaster (Diptera)
Apis mellifera (Hymenoptera)
Capitella teleta (Annelida)
Helobdella robusta (Annelida)
Lottia gigantea (Mollusca)
Octopus bimaculoides (Mollusca)
Strigamia maritima (Myriapoda)
Schistosoma mansoni (Platyhelminthes)
Caenorhabditis elegans (Roundworm)
Drosophila melanogaster (Fruit fly)
Strongylocentrotus purpuratus (Echinodermata)
Amphimedon queenslandica (Porifera)
Trichoplax adhaerens (Placozoa)
Nematostella vectensis (Cnidaria)

Plants

Mnemiopsis leidyi (Ctenophora)
Cyanidioschyzon merolae (Rhodophyta)
Chlamydomonas reinhardtii (Chlorophyta)
Selaginella moellendorffii (Lycopodiophyta)
Marchantia polymorpha (Embryophyta)
Amborella trichopoda (Amborellales)
Arabidopsis thaliana (eudicotyledons)
Solanum lycopersicum (eudicotyledons)
Vitis vinifera (eudicotyledons)
Oryza sativa Japonica (Liliopsida)
Brachypodium distachyon (Liliopsida)
Physcomitrella patens (Bryophyta)

Fungi

Saccharomyces cerevisiae (Baker's yeast)
Aspergillus nidulans (Eurotiales)
Neurospora crassa (Sordariales)
Schizosaccharomyces pombe (Schizosaccharomycetales)
Zymoseptoria tritici (Capnodiales)
Puccinia graminis (Pucciniales)
Ustilago maydis (Ustilaginales)
Dictyostelium discoideum

SAR - a.k.a. weird stuff

Giardia lamblia (Amoebozoa)
Guillardia theta (Cryptophyta)
Emiliania huxleyi (Haptophyceae)
Cryptomonas paramecium (Cryptophyta)
Leishmania major (Kinetoplastida)
Monosiga brevicollis (Choanoflagellida)
Tetrahymena thermophila (Alveolata)
Plasmodium falciparum (Alveolata)
Phytophthora infestans (Stramenopiles)
Phaeodactylum tricornutum (Stramenopiles)
Bigelowiella natans (Rhizaria)