• BLAST: BLAST finds regions of similarity between biological sequences (at NCBI).
• Entrez: cross-database search engine (at NCBI).
• EMBOSS: A high-quality package of free, Open Source software for molecular biology.
• PHYLIP: PHYLogeny Inference Package.

• Entrez: fungi genome projects (at NCBI).
• MIPS: Munich Information Center for Protein Sequences.
• SGD: Saccharomyces Genome Database.
• Genolist: GenoList Genome Browser.
• Gene Census: Comparative genomics - Yale Gerstein Lab.
• Genoscope: French National Sequencing Center.
• CIRM: Centre International de Ressources Microbiennes.
• GOLD: Genomes OnLine Database.
• Index Fungorum: Classification of fungal species.

Sanger Institute  

www.genedb.org  www.sanger.ac.uk

• Schizosaccharomyces pombe
  Wood V, et al. The genome sequence of Schizosaccharomyces pombe. Nature. 2002 Feb 21;415(6874):871-80. Erratum in: Nature
  2003 Jan 2;421(6918):94. Cerrutti L. PMID: 11859360
• Candida dubliniensis
• Candida parapsilosis
• Gene Census: Comparative genomics - Yale Gerstein Lab.

Broad Institute  

www.broad.mit.edu

• Aspergillus nidulans: Aspergillus Sequencing Project. Broad Institute of MIT and Harvard.
• Aspergillus terreus: Aspergillus terreus Sequencing Project. Broad Institute of MIT and Harvard.
• Botrytis cinerea: Botrytis cinerea Sequencing Project. Broad Institute of MIT and Harvard.
• Candida guilliermondii: Candida guilliermondii Sequencing Project. Broad Institute of MIT and Harvard.
• Candida lusitaniae: Candida lusitaniae Sequencing Project. Broad Institute of MIT and Harvard.
• Candida tropicalis: Candida tropicalis Project. Broad Institute of MIT and Harvard.
• Chaetomium globosum: Chaetomium globosum Sequencing Project. Broad Institute of MIT and Harvard.
• Coccidioides immitis: Coccidioides immitis Sequencing Project. Broad Institute of MIT and Harvard.
• Cryptococcus neoformans: Cryptococcus neoformans Sequencing Project. Broad Institute of MIT and Harvard.
• Histoplasma capsulatum: Histoplasma capsulatum Sequencing Project. Broad Institute of MIT and Harvard.
• Kluyveromyces waltii: Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004 Apr 8;428(6983):617-24. Epub 2004 Mar 07. PMID: 15004568: Kluyveromyces waltii Sequencing Project. Broad Institute of MIT and Harvard
• Magnaporthe grisea: Magnaporthe grisea Sequencing Project. Broad Institute of MIT and Harvard.
• Neurospora crassa: Galagan, James E. et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422, 859 - 868 (2003)
• Saccharomyces bayanus: Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241-54. PMID: 12748633.<
• Saccharomyces mikatae: Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241-54. PMID: 12748633.
• Saccharomyces paradoxus: Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241-54. PMID: 12748633.
• Ustilago maydis: Ustilago maydis Sequencing Project. Broad Institute of MIT and Harvard.

Washington University  

http://genome.wustl.edu

• Saccharomyces kudriavzevii: Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 2003 Jul 4;301(5629):71-6. Epub 2003 May 29. PMID: 12775844.
• Saccharomyces kluyveri
• Saccharomyces castellii: Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 2003 Jul 4;301(5629):71-6. Epub 2003 May 29. PMID: 12775844.
• Blastomyces dermatitidis
• Histoplasma capsulatum

Others  

• Saccharomyces cerevisiae:
  Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. Life with 6000 genes. Science. 1996 Oct 25;274(5287):546, 563-7. Review. PMID: 8849441
  [MIPS] / [SGD]
• Ashbya gossypii:
  Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004 Apr 9;304(5668):304-7. Epub 2004 Mar 04. PMID: 15001715
  [AGD]
• Candida albicans:
  Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S. The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A. 2004 May 11;101(19):7329-34. Epub 2004 May 03. PMID: 15123810
  [Pasteur Institute] / [Stanford University]
• Pichia stipitis:
  [Joint Genome Institute]