Downloads & supplementary material

molecular phylogeny of arbuscular mycorrhizal fungi (AMF)

Alignments in FASTA format, the first sequence is the mask used for the analyses (X = sites used):

• SSU alignment used for Figure 2 phylogenetic tree (version 1, Dec 18, 2011)
• SSU-ITSregion-LSU alignment used for Figure 1 & Figures 3-5 phylogenetic trees (version 1, Dec 18, 2011).
  Note that those consensus sequences shown in the annotations of Figs. 3-5 that were already used for the analysis in Fig.1, are not included (as they are identical and thus redundant). Masks are not given (differ slightly for each analysis) but can be easily constructed. The  gene regions are separated by spacers composed of ~~~~ characters (usually no problem, but if your program does not like this character, you maybe need to delete).
• Note that we will refine the alignment further, and update it. We had to change some taxonomic names and culture-annotations after the trees were computed, so in fact there might be some of the 'old' metadata present in the files (although it was checked). We will correct if things need to be updated - please also relate to the supplementary table in the publication, which is up to date. Here, we will note date and a "version number" when a new version is provided, so you can easily identify new or updated data.

Alignments in FASTA format, the first sequence is the mask used for the analyses (0 = not used, X = used sites):

• Alignment used for Figure 1 phylogenetic tree
• Alignment used for Figure 2 phylogenetic tree

Alignments in FASTA format, the first sequence is the mask used for the analyses (- = not used, * = used sites):

• FASTA and Nexus format alignments used for SSU analyses (phylogenetic tree in Fig. 2)
• FASTA and Nexus format alignments used for LSU analyses (phylogenetic tree in Fig. 3)
• FASTA and Nexus format alignments used for ITS analyses (phylogenetic tree in Fig. 4)
• FASTA and Nexus format alignments used for SSU including environmental sequences analyses (phylogenetic tree in Fig. 5)
• Table S1 (was temporary lacking in the NP supplementary online-material, will be fixed, but you can also download it here)

Supplementary material and some information on contaminants & problematic AMF rDNA sequences were shown on the 'contaminant problems' pages, but we have inactivated those, as most of the problems are now widely known. The problems will all be solved by a curated database setup in 2011, in international collaboration, which will be open to the scientific community.

Alignment of 56 AMF sequences, Mortierella and Endogone as outgroup, with longest mask for sites used in the analyses shown (first sequence: - = not used, T = used sites; shorter sets were also analysed):

• EMBL-(CLUSTAL W) format (FTP link): ALIGN_000208  
• PHYLIP-format: PHYLIP_000208

Alignment of 56 AMF sequences, Mortierella and Endogone as outgroup, with longest mask for sites used in the analyses shown  (first sequence: - = not used, T = used sites; shorter sets were also analysed):

• EMBL-(CLUSTAL W) format (FTP link): ALIGN_000124
• PHYLIP-format: PHYLIP_000124
• PAUP-format: PAUP_000124
• Used sequences: Table 000124