References

1. Eisen JA, Fraser CM: Phylogenomics: intersection of evolution and genomics.

   Science 2003, 300(5626):1706-1707. PubMed Abstract | Publisher Full Text

2. Reyes-Prieto A, Hackett JD, Soares MB, Bonaldo MF, Bhattacharya D: Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions.

   Curr Biol 2006, 16(23):2320-2325. PubMed Abstract | Publisher Full Text

3. Frickey T, Lupas AN: PhyloGenie: automated phylome generation and analysis.

   Nucleic Acids Res 2004, 32(17):5231-5238. PubMed Abstract | Publisher Full Text | PubMed Central Full Text

4. Hanekamp K, Bohnebeck U, Beszteri B, Valentin K: PhyloGena – a userfriendly system for automated phylogenetic annotation of unknown sequences.

   Bioinformatics 2007, 23(7):793-801. PubMed Abstract | Publisher Full Text

5. Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D: A molecular timeline for the origin of photosynthetic eukaryotes.

   Mol Biol Evol 2004, 21(5):809-818. PubMed Abstract | Publisher Full Text

6. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D: Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus.

   Proc Natl Acad Sci USA 2002, 99(19):12246-12251. PubMed Abstract | Publisher Full Text | PubMed Central Full Text

7. Sato N, Ishikawa M, Fujiwara M, Sonoike K: Mass identification of chloroplast proteins of endosymbiont origin by phylogenetic profiling based on organism-optimized homologous protein groups.

   Genome Inform 2005, 16(2):56-68. PubMed Abstract

8. Reyes-Prieto A, Weber AP, Bhattacharya D: The origin and establishment of the plastid in algae and plants.

   Annu Rev Genet 2007.PubMed Abstract | Publisher Full Text

9. Li S, Nosenko T, Hackett JD, Bhattacharya D: Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the chromalveolates.

   Mol Biol Evol 2006, 23(3):663-674. PubMed Abstract | Publisher Full Text

10. Nosenko T, Lidie KL, Van Dolah FM, Lindquist E, Cheng JF, Bhattacharya D: Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis.

    Mol Biol Evol 2006, 23(11):2026-2038. PubMed Abstract | Publisher Full Text

11. PHYLIP [http://evolution.genetics.washington.edu/phylip.html]

    

12. PAUP* [http://paup.csit.fsu.edu/]

    

13. Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

    Syst Biol 2003, 52(5):696-704. PubMed Abstract | Publisher Full Text

14. Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

    Bioinformatics 2006, 22(21):2688-2690. PubMed Abstract | Publisher Full Text

15. Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity.

    BMC Bioinformatics 2004, 5:113. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text

16. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

    Nucleic Acids Res 1994, 22(22):4673-4680. PubMed Abstract | Publisher Full Text | PubMed Central Full Text

17. Sipser M: Introduction to the theory of computation. 2nd edition. Course Technology; 2005:31-90.

18. Zmasek CM, Eddy SR: ATV: display and manipulation of annotated phylogenetic trees.

    Bioinformatics 2001, 17(4):383-384. PubMed Abstract | Publisher Full Text

19. Black K, Buikema WJ, Haselkorn R: The hglK gene is required for localization of heterocyst-specific glycolipids in the cyanobacterium Anabaena sp. strain PCC 7120.

    J Bacteriol 1995, 177(22):6440-6448. PubMed Abstract | Publisher Full Text | PubMed Central Full Text

20. Cyanophora Genome Project [http://cyanophora.biology.uiowa.edu]

    

21. Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T: Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.

    Nature 2004, 428(6983):653-657. PubMed Abstract | Publisher Full Text

22. Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup O, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MF: The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.

    J Eukaryot Microbiol 2005, 52(5):399-451. PubMed Abstract | Publisher Full Text

23. Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

    Nucleic Acids Res 2007, (35 Database):D61-65. PubMed Abstract | Publisher Full Text | PubMed Central Full Text

24. Washington University BLAST (WU BLAST) [http://blast.wustl.edu/]

    

25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

    Nat Genet 2000, 25(1):25-29. PubMed Abstract | Publisher Full Text

26. blast2go.pl [http://cyanophora.biology.uiowa.edu/software/blast2go.pl]

    

27. Drawtree: Create PDF or EPS figures of phylogenetic trees [http://www.phylodiversity.net/rree/drawtree/]