Form 1 2020 NCBI Tree Viewer Survey

Tree Viewer Survey MR-123
Tree Display Survey

OMB Control Number: 0925-0648
Expiration Date: 05/31/2021
Public reporting burden for this collection of information is estimated to average 7 minutes per response,
including the time for reviewing instructions, searching existing data sources, gathering and maintaining the
data needed, and completing and reviewing the collection of information. An agency may not conduct or
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valid OMB control number. Send comments regarding this burden estimate or any other aspect of this
collection of information, including suggestions for reducing this burden, to NIH, Project clearance Branch,
6705 Rockledge Drive, MSC 7974, Bethesda, MD 20892-7974, ATTN: PRA (0925-0648). Do not return the
completed form to this address.

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Tree Viewer Survey MR-123
Tree Display Survey, General

1. Which professional category best describes you? Please select only one.
Life Science Researcher

Bioinformatics Professional

Geneticist

Computer Scientist / Software Developer

Genetic Counselor

Educator

Clinical Testing Laboratory Staff

Student

Physician

Librarian / Information Specialist

Other Healthcare Professional

Patient / Family of Patient

Other (please specify)

2. Pick one category that best describes your organization
College or University
Commercial or Industry
Hospital / Clinical / Medical Practice
Non-Profit Organization
Government
Other (please specify)

3. What is your primary reason for visiting the page today?

4. Please outline the workflow that you use with the data you are seeking today at NCBI, including other NCBI
and non-NCBI resources used.

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5. Did you plan to use the tree display in your visit to this page today?
Yes
No

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Tree Viewer Survey MR-123
Tree Display Survey, Current page

6. How easy was it to use the tree display to accomplish your planned task(s)?
Very easy
Easy
Somewhat easy
Neither easy nor difficult
Somewhat difficult
Difficult
Very difficult

7. Given the primary purpose of your visit to this page, what features of a tree display do you find most
important, regardless of whether you used this feature today? Please check all that apply.
node labels
search tree
filter tree (by various data attributes)
sort tree (by various data attributes)
highlight nodes/branches
compress/expand nodes/branches
tree navigation (e.g. pan, zoom)
change tree layout (e.g. circular, rectangular)
an overview of tree displayed at all zoom levels
publication quality image generation
download data in commonly used tree formats
upload and display other trees for comparison to the one provided by NCBI
upload and display approximate location of new (user-supplied) data in the tree
get a list of terminal nodes for a selected internal node
Other (please specify)

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8. Which of the following tree-related features that are under development would you find useful (check all that
apply)?
View kingdom-wide trees for GenBank bacterial, fungal and/or protist assemblies
Download kingdom-wide trees for GenBank bacterial, fungal and/or protist assemblies
View trees for prokaryotic 16S rRNA sequences, fungal ITS (Intergenic Transcribe Spacer) rRNA sequences, and/or fungal 28S
rRNA sequences
Download trees for prokaryotic 16S rRNA sequences, fungal ITS (Intergenic Transcribe Spacer) rRNA sequences, and/or fungal
28S rRNA sequences
Other (please specify)

9. Would you like more information on the algorithm used to generate the tree on this page?
Yes
No
If yes, please tell us what information you would like.

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Tree Viewer Survey MR-123
Tree Display Survey, Databases (a)

10. Which of the following tree-related features that are under development would you find useful (check all
that apply)?
View kingdom-wide trees for GenBank bacterial, fungal and/or protist assemblies
Download kingdom-wide trees for GenBank bacterial, fungal and/or protist assemblies
View trees for prokaryotic 16S rRNA sequences, fungal ITS (Internal Transcribed Spacer) rRNA sequences, and/or fungal 28S
rRNA sequences
Download trees for prokaryotic 16S rRNA sequences, fungal ITS (Internal Transcribed Spacer) rRNA sequences, and/or fungal 28S
rRNA sequences
Other (please specify)

11. Do you use tree displays offered in any of these other NCBI resources? (check all that apply)
BLAST results
COBALT results
SmartBLAST
NCBI Virus
Pathogen Detection Isolates Browser
Genome Workbench
Entrez Genome
None
Other (please specify)

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Tree Viewer Survey MR-123

12. Pick the scale of the dataset you typically visualize in your analyses
10
100
1000
>1000

13. Please describe further how you use the tree display in the resource(s) you selected. Please select all that
apply.
to identify a dataset to build your own tree for the same data
to identify a dataset for comparison to an unsubmitted sequence by BLAST
to identify a dataset for comparison to an unsubmitted sequence through phylogenetic tree building
to identify one or more genome assemblies or annotations for use in some other sequence analysis (not for tree building or
comparison to an unsubmitted sequence)
to examine relationships/identify patterns/exceptions within genome assemblies/sequences for an organism
to download image of tree (e.g. PDF file)
to download tree data (e.g. Newick file)
Other (please specify)

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Tree Viewer Survey MR-123
Tree Building Frequency

14. How often do you build trees?
Never
Sometimes
Often

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Tree Viewer Survey MR-123
Tree Display Survey, tree building

15. When building a tree, what is more important to you?
Speed of rendering is more important than accuracy
Accuracy of the tree is more important than speed
Speed and accuracy are equally important

16. What type of tree building algorithms are you interested in? (check all that apply)
Distance matrix based (e.g. neighbor joining, least squares, minimum evolution)
Maximum likelihood
Parsimony
Bayesian
Other (please specify)

17. What other tools do you use to build your phylogenetic trees and what do you like or not like about them?

18. When visualizing a phylogenetic tree that you have built, what tool features are most important? Please
check all that apply.
Support for custom annotation of nodes and branches
Download/export tree data in popular formats
Navigation options
Share tree online
Create publication quality image
Visualize supporting alignments in context of tree display
Support for different tree layout options (e.g. unrooted trees, unscaled branch lengths)
Other (please specify)

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Tree Viewer Survey MR-123
Tree Display Survey, more feedback

19. How likely is it that you would recommend NCBI's Tree Displays to a friend or colleague?
Not at all likely
0

Extremely likely
1

2

3

4

5

6

7

8

9

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20. Is there anything else you'd like to tell us?

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Tree Viewer Survey MR-123
Tree Display Survey, write to us

Please write to us at [email protected] if you would like to provide additional
feedback on NCBI's tree displays.

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